World fragmentation/chunk duplication

Hello. I am having a horrible problem right now. As soon as I logged in to my server and went to the normal "world", my console started throwing these errors so fast I had to disconnect so they'd stop so I could copy them. Here is an extremely short snippit of it.

Code:

14:27:50 [INFO] Chunk (24, -8) stored at  (11, -30)
14:27:50 [INFO] net.minecraft.server.Chunk
14:27:50 [SEVERE] java.lang.Throwable
14:27:50 [SEVERE]       at net.minecraft.server.ChunkProviderServer.getOrCreateChunk(ChunkProviderServer.java:124)
14:27:50 [SEVERE]       at net.minecraft.server.World.getChunkAt(World.java:272)
14:27:50 [SEVERE]       at net.minecraft.server.World.j(World.java:1852)
14:27:50 [SEVERE]       at net.minecraft.server.World.doTick(World.java:1706)
14:27:50 [SEVERE]       at net.minecraft.server.MinecraftServer.h(MinecraftServer.java:441)
14:27:50 [SEVERE]       at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:361)
14:27:50 [SEVERE]       at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
14:27:50 [INFO] Chunk (17, -30) stored at  (7, -16)
14:27:50 [SEVERE] java.lang.Throwable
14:27:50 [SEVERE]       at org.bukkit.craftbukkit.util.LongHashtable.get(LongHashtable.java:32)
14:27:50 [SEVERE]       at net.minecraft.server.ChunkProviderServer.getOrCreateChunk(ChunkProviderServer.java:116)
14:27:50 [SEVERE]       at net.minecraft.server.World.getChunkAt(World.java:272)
14:27:50 [SEVERE]       at net.minecraft.server.World.j(World.java:1852)
14:27:50 [SEVERE]       at net.minecraft.server.World.doTick(World.java:1706)
14:27:50 [SEVERE]       at net.minecraft.server.MinecraftServer.h(MinecraftServer.java:441)
14:27:50 [SEVERE]       at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:361)
14:27:50 [SEVERE]       at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)
14:27:50 [INFO] Chunk (17, -30) stored at  (7, -16)
14:27:50 [INFO] net.minecraft.server.Chunk
14:27:50 [SEVERE] java.lang.Throwable
14:27:50 [SEVERE]       at net.minecraft.server.ChunkProviderServer.getOrCreateChunk(ChunkProviderServer.java:124)
14:27:50 [SEVERE]       at net.minecraft.server.World.getChunkAt(World.java:272)
14:27:50 [SEVERE]       at net.minecraft.server.World.j(World.java:1852)
14:27:50 [SEVERE]       at net.minecraft.server.World.doTick(World.java:1706)
14:27:50 [SEVERE]       at net.minecraft.server.MinecraftServer.h(MinecraftServer.java:441)
14:27:50 [SEVERE]       at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:361)
14:27:50 [SEVERE]       at net.minecraft.server.ThreadServerApplication.run(SourceFile:422)

and so on. Flying around the world in single player (I copied the map over to my local computer to look around) there are tons of duplicated chunks in random places..

[INFO]
I am running the newest CraftBukkit (build 1000) on Ubuntu 11.04 x86. I have tried going back to Bukkit 953. I get the same issue with and without all my plugins. I have even tried different java versions (I normally use 1.7, I went back to 1.6 update 26). I do all my work through SSH.

Could anyone please help solve this? I really don't want to make a new world and tell all my friends they have to rebuild

I am fine with deleting the duplicated chunks since my city doesn't have any errors in it (all the issues are just outside). As long as I can keep the part we've been building on, it will be fine.

Is there a way to delete chunks and have minecraft regenerate them?

Never mind. I fixed it with Chunkster. Looks a little strange where the errors were, but it works!

EDIT by Moderator: merged posts, please use the edit button instead of double posting.