* Noggit terraforming doesn't work properly. Sometimes it creates a king of "sharp" edges. I wish I could provide a pic now. I will do it later when I am on my PC.
* Sometimes WMOs disappear after saving.
* Some models disappear in the game. (I believe it has smth to do with model UIDs, like the duplication bug).
* Noggit crashes after it reaches a certain amount of memory. (Not a really serious problem).
* If you paint textures with the pressure less then 50, textures don't appear the right way in the game. There are a kind of big crosses on the chunk borders. (It can be fixed manually but it's still a bug.)
* Noggit doesn't render "big alpha" alphamaps on maps like Northrend.
And you always close noggit after save? And reopen it.