This server is running CraftBukkit version git-Bukkit-1.5.2-R0.1-b2771jnks (MC: 1.5.2) (Implementing API version 1.5.2-R0.1)

java.lang.NoClassDefFoundError: org/bukkit/craftbukkit/v1_5_R2/CraftChunk
at com.ryanmichela.giantcaves.GiantCavePopulator.populate(GiantCavePopulator.java:72)
at net.minecraft.server.v1_5_R3.ChunkProviderServer.getChunkAt(ChunkProviderServer.java:238)
at net.minecraft.server.v1_5_R3.Chunk.a(Chunk.java:800)
at net.minecraft.server.v1_5_R3.ChunkProviderServer.getChunkAt(ChunkProviderServer.java:142)
at net.minecraft.server.v1_5_R3.PlayerChunk.(PlayerChunk.java:24)
at net.minecraft.server.v1_5_R3.PlayerChunkMap.a(PlayerChunkMap.java:69)
at net.minecraft.server.v1_5_R3.PlayerChunkMap.b(PlayerChunkMap.java:144)
at net.minecraft.server.v1_5_R3.PlayerChunkMap.movePlayer(PlayerChunkMap.java:220)
at net.minecraft.server.v1_5_R3.PlayerList.d(PlayerList.java:246)
at net.minecraft.server.v1_5_R3.PlayerConnection.a(PlayerConnection.java:422)
at net.minecraft.server.v1_5_R3.Packet10Flying.handle(SourceFile:136)
at net.minecraft.server.v1_5_R3.NetworkManager.b(NetworkManager.java:292)
at net.minecraft.server.v1_5_R3.PlayerConnection.d(PlayerConnection.java:109)
at net.minecraft.server.v1_5_R3.ServerConnection.b(SourceFile:35)
at net.minecraft.server.v1_5_R3.DedicatedServerConnection.b(SourceFile:30)
at net.minecraft.server.v1_5_R3.MinecraftServer.r(MinecraftServer.java:581)
at net.minecraft.server.v1_5_R3.DedicatedServer.r(DedicatedServer.java:226)
at net.minecraft.server.v1_5_R3.MinecraftServer.q(MinecraftServer.java:477)
at net.minecraft.server.v1_5_R3.MinecraftServer.run(MinecraftServer.java:410)
at net.minecraft.server.v1_5_R3.ThreadServerApplication.run(SourceFile:573)
Caused by: java.lang.ClassNotFoundException: org.bukkit.craftbukkit.v1_5_R2.CraftChunk
at org.bukkit.plugin.java.PluginClassLoader.findClass0(PluginClassLoader.java:70)
at org.bukkit.plugin.java.PluginClassLoader.findClass(PluginClassLoader.java:53)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 20 more

Could not reproduce crash with 1.5.2 and CB#2771, see log:

E:\Projects\Java#CraftBukkit Test Area>java.exe -jar "E:\Projects\Java#CraftBukkit Test Area\craftbukkit 1.5.2-R0.1 #2771.jar"
229 recipes
27 achievements
03:15:02 [INFO] Starting minecraft server version 1.5.2
03:15:02 [INFO] Loading properties
03:15:02 [INFO] Default game type: CREATIVE
03:15:02 [INFO] Generating keypair
03:15:03 [INFO] Starting Minecraft server on *:25565
03:15:03 [INFO] This server is running CraftBukkit version git-Bukkit-1.5.2-R0.1-b2771jnks (MC: 1.5.2) (Implementing API version 1.5.2-R0.1)
03:15:03 [INFO] [GiantCaves] Loading GiantCaves v2.2
03:15:03 [INFO] [GiantCaves] Enabling GiantCaves v2.2
03:15:03 [INFO] Preparing level "world"
03:15:03 [INFO] [GiantCaves] Attaching cave populator to world "world"
03:15:03 [INFO] Preparing start region for level 0 (Seed: -8551094949721159217)
03:15:04 [INFO] Server permissions file permissions.yml is empty, ignoring it
03:15:04 [INFO] Done (1,141s)! For help, type "help" or "?"
03:15:48 [INFO] Disconnecting Xaymar [/127.0.0.1:57334]: Outdated client!
03:16:45 [INFO] Xaymar[/127.0.0.1:57356] logged in with entity id 13 at ([world] -1405.2679722461985, 66.0, -817.4718495025412)
03:19:34 [INFO] Connection reset
03:19:34 [INFO] Xaymar lost connection: disconnect.quitting
03:19:56 [INFO] Xaymar [/127.0.0.1:57380] lost connection
03:20:00 [INFO] Xaymar[/127.0.0.1:57387] logged in with entity id 287 at ([world] -1356.0047005286517, 101.0, -456.8781141498917)
03:20:56 [INFO] Xaymar [/127.0.0.1:57380] lost connection

I walked far enough out to generate completely new chunks, yet no crash appeared. So, please, fix you panel or whatever you are using to upload Giant Caves because it clearly is not working right.

And another time, because you showed this behaviour already a few times:
You are currently using a 1.5.1 build with CB#2771, not as you stated a 1.5.2 build with CB#2771. How can I tell? Check your exception log, it shows references to 1.5.1 and not 1.5.2. The 1.5.2 build would error at compilation if those existed.

Come on now, I thought you know better than using incompatible versions. The lines don't even match up between 1.5.1 and 1.5.2 (for obvious reasons). So why are you doing this?

I'm running GiantCaves-1.5.2-R0.1.jar on Bukkit-1.5.2-R0.1

It would seem to me these should be compatible.

That is what they should be. But it states that it can't find a 1.5.1 class:

java.lang.NoClassDefFoundError: org/bukkit/craftbukkit/v1_5_R2/CraftChunk
at com.ryanmichela.giantcaves.GiantCavePopulator.populate(GiantCavePopulator.java:72)

If you send the 1.5.2 jar through a decompiler, you will see not one reference to a 1.5.1 class, only 1.5.2 classes:

import net.minecraft.server.v1_5_R3.ChunkSection;
import net.minecraft.server.v1_5_R3.WorldProvider;
import org.bukkit.craftbukkit.v1_5_R3.CraftChunk;
... (71)
net.minecraft.server.v1_5_R3.Chunk nmsChunk = ((CraftChunk)source).getHandle();
ChunkSection[] chunkSections = nmsChunk.i();

You see, not only do your values and mine not match up, there is not even a single mention of v1_5_R2 in the entire file.

Edit: Misread a word.