Chunks get overwritten, but they aren't corrupted

Hello, I noticed a few days ago that I had a portion on my world that keeps getting deleted / regenerated, I'll give you a quick headsup what all happened:

The world was already generated from all the way back to I think Minecraft 1.2 and we kept it all the way up to 1.8. But ever since I updated to 1185, theres this portion on the map that gets overwritten with the new terrain generation. I tried to place a few blocks in those chunks, saved the map, did a server restart, only to see that the blocks i placed were removed.

The place in question is very ireggular shaped (its not a perfect square) and they all have the same issue. The place covers well over 300 chunks (I got the coordinates with worldedit).

I have absolotely no clue what can cause this, tried disabling some plugins which I thought they would alter the terrain or affect chunks in anyway, and the error still persists.

A scan with Chunkster didn't give any chunk errors as well.

The location goes from Chunk -65,-369 all the way to -33,-384