It's a known issue, caused by missing mcnk chunks. Basically, the adt's don't have all their position data and noggit can't figure out how to arrange the terrain data. Oddly enough, the WoW client doesn't actually care about this data. Ideally, Noggit should be able to act the same way, but I have no idea how to implement such a change.
Last year sometime, I spent something like 2 days trying to get offset fix to only fix the terrain chunks and not modify the model/doodad data, but none of my test cases worked out properly. I'm not a programmer, but have some ideas as to how programs function - offsetfix is an incredibly simple program that just reads in the data chunks, runs a function on the data, and puts everything back together. I have tried to just isolate the MCNK bits and make it do its magic, but to no avail, the model data gets scrubbed, or in one test case, shifted off the map data. There's certainly something I'm missing - the two should be linked together in terms of the coordinates for all assets tied to an ADT.
If I have some free time, I'll take another stab at it sometime soon(tm).