Since I'm working with a project, I don't have all the details or steps to reproduce yet but still wanted to check in... Basically, when working with atlas maker it's corrupting the texture.
I have a 1024x1024 texture atlas which is almost full. When I add a new image to that atlas, instead of going to 1024x2048 it stays at 1024x1024 and all the current textures in it get's corrupted.
Corrupted means all textures showing 1/4 of lover left corner.
I've tried creating a whole new atlas with those images but the result is the same.
For now I've switched to texture packer which luckily I had a license. Btw, TP integration of NGUI is working perfectly.

That is Unity 3.5.2 on Win using NGUI 2.0.7c