Using the most up to date version of AE 2014.
Suddenly (today) No other windows or application will display over the After Effects application window.
I will drag a window (explorer, or Acrobat, or whatever) from my other monitor and it disappears under the After Effects window. If I have Photoshop open on the same monitor I cannot bring it to the front. I have to minimize AE in order to access any other window. This problem is only with AE.
I did look through various preferences (app & system) to see if some "Always on top" option had somehow been activated but didn't see anything.
Do you have hardware accelerate panels turned on?
I did. The problem went away on a reboot but maybe turning that feature off will stop it from happening again. Not even sure why it was turned on to begin with.
I prefer it being on - makes things snappier. Just keep it in mind if the issue crops up again.