I've got a problem with UIAtlas and setting it to reference but I'm not sure if it's NGUI that's broken or just Unity RC1 so hopefully someone can test this for me and report back.
All I do is create a new atlas, select it in the inspector, set the type to reference, de-select the atlas, select it again and it's reverted to a 'normal' atlas. Also when I set it to a reference atlas I can't set it back to normal (without it doing itself after deselecting it).
I'm 99% sure it's Unity but I just have to check. Yay for being on the bleeding edge...