Ubuntu 12.04, 64bit. (Compiz+Unity) Steam notifications forces game to run in window. It is extreamly uncomfortable and disabling steam community does not help. There is also no way to return window to fullscreen as alt+enter is not working, and there is no maximize button.
Hmm, this is a new problem as far as I'm aware. I'll file it in our bugtracker, but meanwhile the only thing I can recommend trying is to run the executable separately (it doesn't require Steam).