So, on upgrade from 14w03b to 14w04b, I started getting a message about the server attempting to save entity NBT. At the point in time, There were item frames that items disappeared from, so I thought that was the problem. I removed the item frames, restarted the server, only to find that the world had not saved where it was before. This ONLY happened in the chunk that the item frames were in. Everything else in the world, except for that chunk saved. I stopped the server, went into MCEdit an removed the item frames. This still did not fix the problem. But I then remembered that, in the same chunk, below where the item frames were, there was the spawn villager trading center. (We had 1 of every type of villager, so to save them from zombification, I set their Invulnerable NBT tag to 1.) So, as far as I can tell, the villagers are preventing ONLY the chunk that they are in to not be saved by the world.

Server Error:

q: Saving entity NBT
        at ru.e(SourceFile:1149)
        at ru.d(SourceFile:1116)
        at arn.a(SourceFile:210)
        at arn.a(SourceFile:99)
        at nl.b(SourceFile:160)
        at nl.a(SourceFile:191)
        at nm.a(SourceFile:655)
        at net.minecraft.server.MinecraftServer.a(SourceFile:295)
        at net.minecraft.server.MinecraftServer.u(SourceFile:479)
        at net.minecraft.server.MinecraftServer.run(SourceFile:377)
        at mc.run(SourceFile:647)
Caused by: java.lang.NullPointerException
        at agx.j(SourceFile:115)
        at agy.a(SourceFile:125)
        at yw.b(SourceFile:212)
        at ru.e(SourceFile:1137)
        ... 10 more

This doesn't seem to be the same crash as the NullPointer Hopper crash

What I expected to happen was...:
Normal server world saving operation

What actually happened was...:
Only the chunk that the affected NBT entities are in does not save.

Steps to Reproduce:
Must be on server
1. Create a villager
2. Use NBTEdit to set said villagers Invulnerable tag to 1
3. Close the world
4. Open the world, place some blocks and /save-all and stop the server.
5. Start up the sever again and you will find that whatever you placed is now gone, but it saved your movement, position, and inventory.

Video:
http://youtu.be/6u6veacFHhk
Updated video showing villager and cleric buginess:
http://youtu.be/x5HysqsuDeQ