Same thing for me, sort of. My gnome-terminals all have a cover cube in them, and not just covering the "terminal" portion, but the menus as well. (gnome-system-monitor too, as the original reporter notes) Disabling the Compiz "Blur Windows" effect fixes this for me. Other plugins seem to have trouble too...the water effect plugin works as long as I hold the activation keys down, but seems to flicker after that. Reassign to compiz-plugins perhaps?
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