The problem is that when I activate one object (in my case it's a button) and deactivate another one and both are at the same position, you can see a blink as if the one button gets deactivated immidiately and the other one is activated the next frame. The behavior is visible using SetActiveRecursively or using NGUITools.
I've already played around with the depth, setting both the same or one below, it doesn't change anything.
Oh, and I use version 2.1.0.