Does this happen with any game for you? I can't reproduce that on my end so far, so I'd be interested to test the exact same scenario causing that on your side.
This bug affected at least CS:GO, Trine 2, No more room in hell and Deponia: The Complete Journey and that as long as I can remember playing these games under ubuntu. The bug also occured when I've done something that brings a libnotify popup onto the screen like changing my system volume. But yesterday evening I installed new catalyst 14.12 (fglrx14.501) and there were some greater updates for xserver and so on and now the bug is gone. I can't reproduce it anymore so this bug-thread can be closed.
Nothing extracted yet.
I can start a game through steam open the steam overlay and there is a mouse cursor as it should be and everythings works fine. But once I minimize the game and maximize it back there's no cursor in the steam overlay any more. In the game everything is still working and I see a mousecursor but in the steam overlay it is invisible. I can still see a button highlighting if I focus it in the overlay but without a visible cursor it's hard to hit something. This bug affects all games and is repeatable.
My system is Ubuntu 14.04 64 bit with AMD R7 260X and catalyst 14.9 (fglrx 14.301)