Hi,
It's not very obvious here but the graphist made some specific things on some sprites that make them non "sliceable" (sorry I don't know if the word exists ^^ )
Same thing for the buttons with texts, if I didn't made a sliced sprite from the assets, the graphist give me, this is because the text, for example, have some effects that I can't reproduce with NGUI.
Anyway, could it be a good idea to split my atlas in two or more parts to prevent me from these Atlas Maker "WTF" problems? (I know by reading the forum that the problem is not from you but from something inside Unity that is fucking the textures during the build)