Same thing is happening to me. This is the same kind of 'update lag' that you usually see only in multiplayer.
This only happens for me after playing in a world from an earlier version. In this case, I generated this amplified world in 1.7.4, then played with it for a while in 1.6.4 (I had gone back to that version for MP, and forgot to go back to 1.7.4 before playing SP). When I remembered and switched back to 1.7.4, the block reappearing happened.
Here's the dev console log:
[07:32:23 INFO]: Refreshing local version list...
[07:32:23 INFO]: Minecraft Launcher 1.3.7 (through bootstrap 5) started on windows...
[07:32:23 INFO]: Current time is Dec 13, 2013 7:32:23 AM
[07:32:23 INFO]: System.getProperty('os.name') == 'Windows 7'
[07:32:23 INFO]: System.getProperty('os.version') == '6.1'
[07:32:23 INFO]: System.getProperty('os.arch') == 'x86'
[07:32:23 INFO]: System.getProperty('java.version') == '1.7.0_45'
[07:32:23 INFO]: System.getProperty('java.vendor') == 'Oracle Corporation'
[07:32:23 INFO]: System.getProperty('sun.arch.data.model') == '32'
[07:32:23 INFO]: Refreshing remote version list...
[07:32:25 INFO]: Refresh complete.
[07:32:25 INFO]: Loaded 1 profile(s); selected 'Excrubulent'
[07:32:25 INFO]: Refreshing auth...
[07:32:25 INFO]: Logging in with access token
[07:32:39 INFO]: Getting syncinfo for selected version
[07:32:39 INFO]: Queueing library & version downloads
[07:32:40 INFO]: Download job 'Version & Libraries' started (16 threads, 27 files)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\net\sf\jopt-simple\jopt-simple\4.5\jopt-simple-4.5.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch-external-platform\4.5\twitch-external-platform-4.5-natives-windows-32.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch-platform\5.12\twitch-platform-5.12-natives-windows-32.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\ibm\icu\icu4j-core-mojang\51.2\icu4j-core-mojang-51.2.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\java3d\vecmath\1.3.1\vecmath-1.3.1.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\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)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl_util\2.9.1-nightly-20131120\lwjgl_util-2.9.1-nightly-20131120.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\net\java\jutils\jutils\1.0.0\jutils-1.0.0.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\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)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\codecwav\20101023\codecwav-20101023.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch\5.12\twitch-5.12.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\google\code\gson\gson\2.2.4\gson-2.2.4.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\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)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\libraryjavasound\20101123\libraryjavasound-20101123.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\apache\commons\commons-lang3\3.1\commons-lang3-3.1.jar for job 'Version & Libraries'... (try 0)
[07:32:40 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl\2.9.1-nightly-20131120\lwjgl-2.9.1-nightly-20131120.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Download job 'Resources' skipped as there are no files to download
[07:32:42 INFO]: Job 'Resources' finished successfully (took 0:00:00.000)
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch-external-platform\4.5\twitch-external-platform-4.5-natives-windows-32.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl\2.9.1-nightly-20131120\lwjgl-2.9.1-nightly-20131120.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\codecjorbis\20101023\codecjorbis-20101023.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\libraryjavasound\20101123\libraryjavasound-20101123.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\net\java\jinput\jinput\2.0.5\jinput-2.0.5.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Attempting to download C:\Users\Goop\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)
[07:32:42 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\soundsystem\20120107\soundsystem-20120107.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\commons-io\commons-io\2.4\commons-io-2.4.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\codecjorbis\20101023\codecjorbis-20101023.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\net\sf\trove4j\trove4j\3.0.3\trove4j-3.0.3.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\google\guava\guava\15.0\guava-15.0.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\mojang\authlib\1.2\authlib-1.2.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\soundsystem\20120107\soundsystem-20120107.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\mojang\authlib\1.2\authlib-1.2.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\librarylwjglopenal\20100824\librarylwjglopenal-20100824.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\librarylwjglopenal\20100824\librarylwjglopenal-20100824.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\versions\1.7.4\1.7.4.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Attempting to download C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl-platform\2.9.1-nightly-20131120\lwjgl-platform-2.9.1-nightly-20131120-natives-windows.jar for job 'Version & Libraries'... (try 0)
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl-platform\2.9.1-nightly-20131120\lwjgl-platform-2.9.1-nightly-20131120-natives-windows.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch\5.12\twitch-5.12.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch-platform\5.12\twitch-platform-5.12-natives-windows-32.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\codecwav\20101023\codecwav-20101023.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl_util\2.9.1-nightly-20131120\lwjgl_util-2.9.1-nightly-20131120.jar for job 'Version & Libraries': Local file matches local checksum, using that
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Finished downloading C:\Users\Goop\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
[07:32:42 INFO]: Finished downloading C:\Users\Goop\AppData\Roaming\.minecraft\versions\1.7.4\1.7.4.jar for job 'Version & Libraries': Used own copy as it matched etag
[07:32:42 INFO]: Job 'Version & Libraries' finished successfully (took 0:00:02.084)
[07:32:42 INFO]: Launching game
[07:32:42 INFO]: Looking for old natives & assets to clean up...
[07:32:42 INFO]: Unpacking natives to C:\Users\Goop\AppData\Roaming\.minecraft\versions\1.7.4\1.7.4-natives-2198961019331
[07:32:43 INFO]: Launching in C:\Users\Goop\AppData\Roaming\.minecraft
[07:32:43 INFO]: Half command: C:\Program Files (x86)\Java\jre7\bin\javaw.exe -XX:HeapDumpPath=MojangTricksIntelDriversForPerformance_javaw.exe_minecraft.exe.heapdump -Xmx512M -Djava.library.path=C:\Users\Goop\AppData\Roaming\.minecraft\versions\1.7.4\1.7.4-natives-2198961019331 -cp C:\Users\Goop\AppData\Roaming\.minecraft\libraries\java3d\vecmath\1.3.1\vecmath-1.3.1.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\net\sf\trove4j\trove4j\3.0.3\trove4j-3.0.3.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\ibm\icu\icu4j-core-mojang\51.2\icu4j-core-mojang-51.2.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\net\sf\jopt-simple\jopt-simple\4.5\jopt-simple-4.5.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\codecjorbis\20101023\codecjorbis-20101023.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\codecwav\20101023\codecwav-20101023.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\libraryjavasound\20101123\libraryjavasound-20101123.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\librarylwjglopenal\20100824\librarylwjglopenal-20100824.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\paulscode\soundsystem\20120107\soundsystem-20120107.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\io\netty\netty-all\4.0.10.Final\netty-all-4.0.10.Final.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\google\guava\guava\15.0\guava-15.0.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\apache\commons\commons-lang3\3.1\commons-lang3-3.1.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\commons-io\commons-io\2.4\commons-io-2.4.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\net\java\jinput\jinput\2.0.5\jinput-2.0.5.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\net\java\jutils\jutils\1.0.0\jutils-1.0.0.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\google\code\gson\gson\2.2.4\gson-2.2.4.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\com\mojang\authlib\1.2\authlib-1.2.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\apache\logging\log4j\log4j-api\2.0-beta9\log4j-api-2.0-beta9.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\apache\logging\log4j\log4j-core\2.0-beta9\log4j-core-2.0-beta9.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl\2.9.1-nightly-20131120\lwjgl-2.9.1-nightly-20131120.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\org\lwjgl\lwjgl\lwjgl_util\2.9.1-nightly-20131120\lwjgl_util-2.9.1-nightly-20131120.jar;C:\Users\Goop\AppData\Roaming\.minecraft\libraries\tv\twitch\twitch\5.12\twitch-5.12.jar;C:\Users\Goop\AppData\Roaming\.minecraft\versions\1.7.4\1.7.4.jar net.minecraft.client.main.Main
[07:32:43 INFO]: Client> [07:32:43] [main/INFO]: Setting user: Excrubulent
[07:32:43 INFO]: Client> [07:32:43] [main/INFO]: (Session ID is token:739bfb6fa2f74f2a99974cb1e55d264f:21f1ce300f8542ccb2bfe45eb784cbc2)
[07:32:44 INFO]: Client> [07:32:44] [Client thread/INFO]: LWJGL Version: 2.9.1
[07:32:44 INFO]: Client> [07:32:44] [Client thread/INFO]: Reloading ResourceManager: Default
[07:32:44 INFO]: Client>
[07:32:44 INFO]: Client> Starting up SoundSystem...
[07:32:45 INFO]: Client> Initializing LWJGL OpenAL
[07:32:45 INFO]: Client> (The LWJGL binding of OpenAL. For more information, see http://www.lwjgl.org)
[07:32:45 INFO]: Client> OpenAL initialized.
[07:32:45 INFO]: Client>
[07:32:45 INFO]: Client> [07:32:45] [Sound Library Loader/INFO]: Sound engine started
[07:32:45 INFO]: Client> [07:32:45] [Client thread/INFO]: Created: 512x256 textures/blocks-atlas
[07:32:45 INFO]: Client> [07:32:45] [Client thread/INFO]: Created: 256x256 textures/items-atlas
[07:32:50 INFO]: Client> [07:32:50] [Server thread/INFO]: Starting integrated minecraft server version 1.7.4
[07:32:50 INFO]: Client> [07:32:50] [Server thread/INFO]: Generating keypair
[07:32:51 INFO]: Client> [07:32:51] [Server thread/INFO]: Preparing start region for level 0
[07:32:52 INFO]: Client> [07:32:52] [Server thread/INFO]: Preparing spawn area: 61%
[07:32:53 INFO]: Client> [07:32:53] [Server thread/INFO]: Changing view distance to 8, from 10
[07:32:53 INFO]: Client> [07:32:53] [Server thread/INFO]: Excrubulent[local:E:4797e69d] logged in with entity id 396 at (930.3000000119209, 187.0, -516.3139580303733)
[07:32:53 INFO]: Client> [07:32:53] [Server thread/INFO]: Excrubulent joined the game
[07:32:58 INFO]: Client> [07:32:58] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 4065ms behind, skipping 81 tick(s)
[07:33:18 INFO]: Client> [07:33:18] [Server thread/INFO]: Saving and pausing game...
[07:33:18 INFO]: Client> [07:33:18] [Server thread/INFO]: Saving chunks for level 'Excrubulence'/Overworld
[07:33:18 INFO]: Client> [07:33:18] [Server thread/INFO]: Saving chunks for level 'Excrubulence'/Nether
[07:33:18 INFO]: Client> [07:33:18] [Server thread/INFO]: Saving chunks for level 'Excrubulence'/The End
[07:33:19 INFO]: Client> [07:33:19] [Server thread/INFO]: Stopping server
[07:33:19 INFO]: Client> [07:33:19] [Server thread/INFO]: Saving players
[07:33:19 INFO]: Client> [07:33:19] [Server thread/INFO]: Saving worlds
[07:33:19 INFO]: Client> [07:33:19] [Server thread/INFO]: Saving chunks for level 'Excrubulence'/Overworld
[07:33:19 INFO]: Client> [07:33:19] [Server thread/INFO]: Saving chunks for level 'Excrubulence'/Nether
[07:33:19 INFO]: Client> [07:33:19] [Server thread/INFO]: Saving chunks for level 'Excrubulence'/The End
[07:33:21 INFO]: Client> [07:33:21] [Client thread/INFO]: Stopping!
[07:33:21 INFO]: Client>
[07:33:21 INFO]: Client> SoundSystem shutting down...
[07:33:21 INFO]: Client> Author: Paul Lamb, www.paulscode.com
[07:33:21 INFO]: Client>
[07:33:21 INFO]: Game ended with no troubles detected (exit code 0)
[07:33:21 INFO]: Deleting C:\Users\Goop\AppData\Roaming\.minecraft\versions\1.7.4\1.7.4-natives-2198961019331
[07:33:21 WARN]: Couldn't delete C:\Users\Goop\AppData\Roaming\.minecraft\versions\1.7.4\1.7.4-natives-2198961019331 - scheduling for deletion upon exit
Michael van Drempt
Same thing is happening to me. This is the same kind of 'update lag' that you usually see only in multiplayer.
This only happens for me after playing in a world from an earlier version. In this case, I generated this amplified world in 1.7.4, then played with it for a while in 1.6.4 (I had gone back to that version for MP, and forgot to go back to 1.7.4 before playing SP). When I remembered and switched back to 1.7.4, the block reappearing happened.
Here's the dev console log: