NullPointerException on server start

I just updated minecraft to 1.4.6, attempted to join singleplayer, and it responded by crashing with the NullPointerException, and told me to report it with the below-pasted crash report.

I then tried again, and got repeated identical errors (as quickly as my console could record them):

Wrong location! pe['Sheep'/2774, l='World 2', x=-221.72, y=64.00, z=-353.37]
java.lang.Exception: Stack trace
	at java.lang.Thread.dumpStack(Thread.java:1342)
	at zz.a(SourceFile:504)
	at yc.a(SourceFile:1343)
	at in.a(SourceFile:450)
	at yc.g(SourceFile:1297)
	at yc.h(SourceFile:1196)
	at in.h(SourceFile:362)
	at net.minecraft.server.MinecraftServer.r(SourceFile:744)
	at net.minecraft.server.MinecraftServer.q(SourceFile:679)
	at bdz.q(SourceFile:117)
	at net.minecraft.server.MinecraftServer.run(SourceFile:613)
	at fy.run(SourceFile:849)

I then noticed that I was trying to use it with a world that had historically had issues (ever since a system failure while the world was running, and I had to recover the world), and tested another world, which worked. I then tested the broken world again, and it also worked.

I keep a git history of my minecraft saves. This allowed me to checkout the older version of the world (`testing`), and test again. The second time, I yet again got a failure. I then ran the known-working world, which worked. When I retried the broken world, it still does not work, and I cannot figure out how to make it work.

However, upon switching back to `master`, the previously broken world works again, though it does complain:

Chunk file at -14,-25 is in the wrong location; relocating. (Expected -14, -25, got -13, -25)
Chunk file at -14,-24 is in the wrong location; relocating. (Expected -14, -24, got -12, -16)
Chunk file at -14,-23 is in the wrong location; relocating. (Expected -14, -23, got -11, -26)
Chunk file at -14,-12 is in the wrong location; relocating. (Expected -14, -12, got -14, -26)

The .tar.bz2 archives are 14M each, and thus I can't upload them.

---- Minecraft Crash Report (Failure 1)----
// Ooh. Shiny.

Time: 12/26/12 7:36 PM
Description: Exception in server tick loop

java.lang.NullPointerException
        at cf.b(SourceFile:103)
        at cf.a(SourceFile:35)
        at iv.b(SourceFile:436)
        at gm.a(SourceFile:72)
        at bec.b(SourceFile:73)
        at net.minecraft.server.MinecraftServer.r(SourceFile:762)
        at net.minecraft.server.MinecraftServer.q(SourceFile:679)
        at bdz.q(SourceFile:117)
        at net.minecraft.server.MinecraftServer.run(SourceFile:613)
        at fy.run(SourceFile:849)


A detailed walkthrough of the error, its code path and all known details is as follows:
---------------------------------------------------------------------------------------

-- System Details --
Details:
        Minecraft Version: 1.4.6
        Operating System: Linux (amd64) version 3.2.0-35-generic
        Java Version: 1.7.0_09, Oracle Corporation
        Java VM Version: OpenJDK 64-Bit Server VM (mixed mode), Oracle Corporation
        Memory: 123544552 bytes (117 MB) / 357892096 bytes (341 MB) up to 1908932608 bytes (1820 MB)
        JVM Flags: 1 total; -Xmx2048m
        AABB Pool Size: 83653 (4684568 bytes; 4 MB) allocated, 83653 (4684568 bytes; 4 MB) used
        Suspicious classes: No suspicious classes found.
        IntCache: cache: 18, tcache: 0, allocated: 3, tallocated: 63
        Profiler Position: N/A (disabled)
        Vec3 Pool Size: 8870 (496720 bytes; 0 MB) allocated, 8870 (496720 bytes; 0 MB) used
        Player Count: 0 / 8; []
        Type: Integrated Server (map_client.txt)
        Is Modded: Probably not. Jar signature remains and both client + server brands are untouched.