So we have a bit of a strange issue.
We have a couple of scenes that have very basic 2D Gui's on them. The issue we have is Buttons on iOS, don't receive OnPress, while on PC and Mac they do.
We have solved the problem by un-checking "Clip Raycasts" from the GUI Camera. Which upon further inspection does actually make sense, because our panel's Z got set to -499 somehow, when our cameras clip range is -2 to 2 (Default).
So the real issue I guess is the inconsistency. The way it works on iOS seems more correct, but then we need the PC and Mac builds to also behave this way.
Unity 4.0.0f7
NGUI 11 15 2012 package