Well....I encountered a very similar situation when I first got 'Neverwinter Nights' running under Linux. The solution I found was in the nwn.ini file to set it like so....
Switching FullScreen to '0' and AllowWindowedMode to '1' took it out of full screen entirely and allowed me to switch desktops at will. The problem is....now I can't really use side-screen turning to rotate the POV in the game. But I'm learning to use the keyboard for more refined control....so it's an acceptable trade to me.
This may or may not be a workable solution for other games.
And....ummm....should I even ask what's going on here? ->