I've been running compiz fusion on Fedora 8 for a while and found that my windows key short-cuts only work half the time; well I found that if I...
add
Option "XkbOptions" "altwin:super_win"to the InputDevice section of my /etc/X11/xorg.conf
It works every time. I've logged in and out of my laptop a few times over the last couple of days and had no problems since.