Common problem with compiz which AFAIK will be fixed some time spring 2009.
What you can do is to if KDE;
kwin --replace
if Gnome
metacity --replace
Then launch the game.
If it works you can build a script to turn off compiz, launch the game, when exiting the game it will start compiz up again.
Another solution is to use fusion-icon, not sure if it works in KDE, but it works in Gnome.