Updated Java, problem persisted.
However, I did some more testing on it, and the problem isn't the hoppers themselves but the other stuff that's hooked up to them. Ie, I left the hoppers churning but disconnected them from the other redstone around them, and that fixed things. So maybe the problem is large-ish (few hundred) block updates right on the edge of loaded/unloaded.
@Samuel: No hopper adjacent chunk borders. Problem persists on "peaceful."
@Kumasasa:
[05:23:54 INFO]: Refreshing local version list...
[05:23:54 INFO]: Minecraft Launcher 1.3.9 (through bootstrap 5) started on windows...
[05:23:54 INFO]: Current time is Feb 9, 2014 5:23:54 AM
[05:23:54 INFO]: System.getProperty('os.name') == 'Windows 7'
[05:23:54 INFO]: System.getProperty('os.version') == '6.1'
[05:23:54 INFO]: System.getProperty('os.arch') == 'amd64'
[05:23:54 INFO]: System.getProperty('java.version') == '1.7.0_25'
[05:23:54 INFO]: System.getProperty('java.vendor') == 'Oracle Corporation'
[05:23:54 INFO]: System.getProperty('sun.arch.data.model') == '64'
[05:23:55 INFO]: Refreshing remote version list...
[05:23:55 INFO]: Refresh complete.
[05:23:55 INFO]: Loaded 2 profile(s); selected 'snapshot'
[05:23:55 INFO]: Refreshing auth...
[05:23:55 INFO]: Logging in with access token
[05:24:15 INFO]: Getting syncinfo for selected version
[05:24:15 INFO]: Queueing library & version downloads
[05:24:15 INFO]: Download job 'Version & Libraries' started (16 threads, 28 files)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl_util\2.9.1\lwjgl_util-2.9.1.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\libraryjavasound\20101123\libraryjavasound-20101123.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch-platform\5.16\twitch-platform-5.16-natives-windows-64.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\java\jinput\jinput-platform\2.0.5\jinput-platform-2.0.5-natives-windows.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\google\guava\guava\15.0\guava-15.0.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\sf\trove4j\trove4j\3.0.3\trove4j-3.0.3.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\mojang\authlib\1.4.2\authlib-1.4.2.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\java\jutils\jutils\1.0.0\jutils-1.0.0.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\commons-io\commons-io\2.4\commons-io-2.4.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\java\jinput\jinput\2.0.5\jinput-2.0.5.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl\2.9.1\lwjgl-2.9.1.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch-external-platform\4.5\twitch-external-platform-4.5-natives-windows-64.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl-platform\2.9.1\lwjgl-platform-2.9.1-natives-windows.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\codecjorbis\20101023\codecjorbis-20101023.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\google\code\gson\gson\2.2.4\gson-2.2.4.jar for job 'Version & Libraries'... (try 0)
[05:24:15 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\apache\logging\log4j\log4j-api\2.0-beta9\log4j-api-2.0-beta9.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Download job 'Resources' skipped as there are no files to download
[05:24:16 INFO]: Job 'Resources' finished successfully (took 0:00:00.000)
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch-external-platform\4.5\twitch-external-platform-4.5-natives-windows-64.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\sf\trove4j\trove4j\3.0.3\trove4j-3.0.3.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\google\guava\guava\15.0\guava-15.0.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl\2.9.1\lwjgl-2.9.1.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\apache\logging\log4j\log4j-api\2.0-beta9\log4j-api-2.0-beta9.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\ibm\icu\icu4j-core-mojang\51.2\icu4j-core-mojang-51.2.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl-platform\2.9.1\lwjgl-platform-2.9.1-natives-windows.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\apache\commons\commons-lang3\3.1\commons-lang3-3.1.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\apache\logging\log4j\log4j-core\2.0-beta9\log4j-core-2.0-beta9.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\sf\jopt-simple\jopt-simple\4.5\jopt-simple-4.5.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\google\code\gson\gson\2.2.4\gson-2.2.4.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\codecjorbis\20101023\codecjorbis-20101023.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\commons-io\commons-io\2.4\commons-io-2.4.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\java\jinput\jinput\2.0.5\jinput-2.0.5.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\java\jutils\jutils\1.0.0\jutils-1.0.0.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch-platform\5.16\twitch-platform-5.16-natives-windows-64.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\java\jinput\jinput-platform\2.0.5\jinput-platform-2.0.5-natives-windows.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\mojang\authlib\1.4.2\authlib-1.4.2.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl_util\2.9.1\lwjgl_util-2.9.1.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\io\netty\netty-all\4.0.10.Final\netty-all-4.0.10.Final.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\libraryjavasound\20101123\libraryjavasound-20101123.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch\5.16\twitch-5.16.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\java3d\vecmath\1.3.1\vecmath-1.3.1.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\librarylwjglopenal\20100824\librarylwjglopenal-20100824.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\codecwav\20101023\codecwav-20101023.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\sf\jopt-simple\jopt-simple\4.5\jopt-simple-4.5.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\soundsystem\20120107\soundsystem-20120107.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\librarylwjglopenal\20100824\librarylwjglopenal-20100824.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\codecwav\20101023\codecwav-20101023.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\libraries\commons-codec\commons-codec\1.9\commons-codec-1.9.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Attempting to download C:\Users\andrew\AppData\Roaming\.minecraft\versions\14w06b\14w06b.jar for job 'Version & Libraries'... (try 0)
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\soundsystem\20120107\soundsystem-20120107.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\apache\commons\commons-lang3\3.1\commons-lang3-3.1.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\commons-codec\commons-codec\1.9\commons-codec-1.9.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch\5.16\twitch-5.16.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\java3d\vecmath\1.3.1\vecmath-1.3.1.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\apache\logging\log4j\log4j-core\2.0-beta9\log4j-core-2.0-beta9.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\ibm\icu\icu4j-core-mojang\51.2\icu4j-core-mojang-51.2.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\libraries\io\netty\netty-all\4.0.10.Final\netty-all-4.0.10.Final.jar for job 'Version & Libraries': Local file matches local checksum, using that
[05:24:16 INFO]: Finished downloading C:\Users\andrew\AppData\Roaming\.minecraft\versions\14w06b\14w06b.jar for job 'Version & Libraries': Used own copy as it matched etag
[05:24:16 INFO]: Job 'Version & Libraries' finished successfully (took 0:00:00.373)
[05:24:16 INFO]: Launching game
[05:24:16 INFO]: Looking for old natives & assets to clean up...
[05:24:16 INFO]: Unpacking natives to C:\Users\andrew\AppData\Roaming\.minecraft\versions\14w06b\14w06b-natives-46105356924553
[05:24:16 INFO]: Launching in C:\Users\andrew\AppData\Roaming\.minecraft
[05:24:16 INFO]: Half command: C:\Program Files\Java\jre7\bin\javaw.exe -XX:HeapDumpPath=MojangTricksIntelDriversForPerformance_javaw.exe_minecraft.exe.heapdump -Xmx1G -Xmx2048M -Xms2048M -Djava.library.path=C:\Users\andrew\AppData\Roaming\.minecraft\versions\14w06b\14w06b-natives-46105356924553 -cp C:\Users\andrew\AppData\Roaming\.minecraft\libraries\java3d\vecmath\1.3.1\vecmath-1.3.1.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\sf\trove4j\trove4j\3.0.3\trove4j-3.0.3.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\ibm\icu\icu4j-core-mojang\51.2\icu4j-core-mojang-51.2.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\sf\jopt-simple\jopt-simple\4.5\jopt-simple-4.5.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\codecjorbis\20101023\codecjorbis-20101023.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\codecwav\20101023\codecwav-20101023.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\libraryjavasound\20101123\libraryjavasound-20101123.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\librarylwjglopenal\20100824\librarylwjglopenal-20100824.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\paulscode\soundsystem\20120107\soundsystem-20120107.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\io\netty\netty-all\4.0.10.Final\netty-all-4.0.10.Final.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\google\guava\guava\15.0\guava-15.0.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\apache\commons\commons-lang3\3.1\commons-lang3-3.1.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\commons-io\commons-io\2.4\commons-io-2.4.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\commons-codec\commons-codec\1.9\commons-codec-1.9.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\java\jinput\jinput\2.0.5\jinput-2.0.5.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\net\java\jutils\jutils\1.0.0\jutils-1.0.0.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\google\code\gson\gson\2.2.4\gson-2.2.4.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\com\mojang\authlib\1.4.2\authlib-1.4.2.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\apache\logging\log4j\log4j-api\2.0-beta9\log4j-api-2.0-beta9.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\apache\logging\log4j\log4j-core\2.0-beta9\log4j-core-2.0-beta9.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl\2.9.1\lwjgl-2.9.1.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl_util\2.9.1\lwjgl_util-2.9.1.jar;C:\Users\andrew\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch\5.16\twitch-5.16.jar;C:\Users\andrew\AppData\Roaming\.minecraft\versions\14w06b\14w06b.jar net.minecraft.client.main.Main
[05:24:17 INFO]: Client> [05:24:17] [main/INFO]: Setting user: extremities
[05:24:17 INFO]: Client> [05:24:17] [main/INFO]: (Session ID is token:305d6a77aada4c729ba64fca06ae30f5:d2c57281a7114b778153c3ce60f0c8dc)
[05:24:18 INFO]: Client> [05:24:18] [Client thread/INFO]: LWJGL Version: 2.9.1
[05:24:18 INFO]: Client> [05:24:18] [Client thread/INFO]: Reloading ResourceManager: Default
[05:24:18 INFO]: Client>
[05:24:18 INFO]: Client> Starting up SoundSystem...
[05:24:19 INFO]: Client> Initializing LWJGL OpenAL
[05:24:19 INFO]: Client> (The LWJGL binding of OpenAL. For more information, see http://www.lwjgl.org)
[05:24:19 INFO]: Client> OpenAL initialized.
[05:24:19 INFO]: Client>
[05:24:19 INFO]: Client> [05:24:19] [Sound Library Loader/INFO]: Sound engine started
[05:24:19 INFO]: Client> [05:24:19] [Client thread/INFO]: Created: 512x256 textures/blocks-atlas
[05:24:19 INFO]: Client> [05:24:19] [Client thread/INFO]: Created: 256x256 textures/items-atlas
[05:24:20 INFO]: Client> [05:24:20] [MCO Availability Checker #1/ERROR]: Couldn't connect to Realms
[05:24:20 INFO]: Client> ceh:
[05:24:20 INFO]: Client> at cdm.a(SourceFile:251) ~[14w06b.jar:?]
[05:24:20 INFO]: Client> at cdm.b(SourceFile:86) ~[14w06b.jar:?]
[05:24:20 INFO]: Client> at bgy.run(SourceFile:206) [14w06b.jar:?]
[05:24:25 INFO]: Client> [05:24:25] [Server thread/INFO]: Starting integrated minecraft server version 14w06b
[05:24:25 INFO]: Client> [05:24:25] [Server thread/INFO]: Generating keypair
[05:24:25 INFO]: Client> [05:24:25] [Server thread/INFO]: Preparing start region for level 0
[05:24:26 INFO]: Client> [05:24:26] [Server thread/INFO]: Changing view distance to 12, from 10
[05:24:26 INFO]: Client> [05:24:26] [Server thread/INFO]: extremities[local:E:b1b53cf9] logged in with entity id 189 at (-377.9610730155365, 31.0, -195.77122247918666)
[05:24:26 INFO]: Client> [05:24:26] [Server thread/INFO]: extremities joined the game
[05:27:36 INFO]: Client> [05:27:36] [Server thread/INFO]: Saving and pausing game...
[05:27:36 INFO]: Client> [05:27:36] [Server thread/INFO]: Saving chunks for level 'updates 1.7'/Overworld
[05:27:36 INFO]: Client> [05:27:36] [Server thread/INFO]: Saving chunks for level 'updates 1.7'/Nether
[05:27:36 INFO]: Client> [05:27:36] [Server thread/INFO]: Saving chunks for level 'updates 1.7'/The End
[05:28:02 INFO]: Client> [05:28:02] [Client thread/INFO]: Warning: Clientside chunk ticking took 5463 ms
[05:28:08 INFO]: Client> [05:28:08] [Client thread/INFO]: Warning: Clientside chunk ticking took 5467 ms
[05:28:17 INFO]: Client> [05:28:17] [Client thread/INFO]: Warning: Clientside chunk ticking took 8049 ms
[05:28:17 INFO]: Client> [05:28:17] [Server thread/INFO]: Saving and pausing game...
[05:28:17 INFO]: Client> [05:28:17] [Server thread/INFO]: Saving chunks for level 'updates 1.7'/Overworld
[05:28:17 INFO]: Client> [05:28:17] [Server thread/INFO]: Saving chunks for level 'updates 1.7'/Nether
[05:28:17 INFO]: Client> [05:28:17] [Server thread/INFO]: Saving chunks for level 'updates 1.7'/The End
It looks as if all my hoppers are in the same chunk in two worlds where i have had this problem (didn't check the third). However, it's fair to point out that they are connected to a lot of redstone and water controlling pistons, not all of which is in the same chunk as them.
I have since tried recreating the bug in creative, but it didn't bug out. I started a new creative world and copy-pasted the whole mob grinder into it at the same Y as the other worlds, and moved away, but only got a minor little lag spike on leaving the area, as opposed to the game-breaking freeze.
However, the 'turn off the clock' fix has worked both the worlds that I tested it on.
I lost the worlds on which it was occurring to a hard disk crash, so I don't know. Apologies.