It seems to me there have been some changes with the way fullscreen programs behave, compared to how it used to be. It now regularly happens to me that if I move my mouse to the left side of the screen while in a fullscreen app/game, my dock (which is set to "always on top") pops up, which it never did before.
So with the AC launcher, it kinda seems as if it appears it is on top of all the other apps, but in reality, when I try to click on it, I'm clicking on whatever's "below it", be it a browser window or a desktop. So it's not really frozen, there just seems to be no way to click on it.
(And no, before anyone asks - my dock isn't the issue, I've tried. I've tried most of what I could think of or what people have suggested on the internet, no dice.)