Just wanted to share something that was giving me fits. I have an swing application in full screen exclusive mode. If I closed a frame (with a still visible frame behind it) the still visible frame would get wonky and minimize; even clicking on it wouldn't maximize it again. Changing the GNOME desktop effects to "None" seems to have fixed this; there is also noticeably less jitter going from frame to frame. Hope it helps!
"The greatest of all weaknesses is the fear of appearing weak." - JB Bossuet