This problem is now solved in ubuntu 9.04.
The trick is to change the following setting.
sudo gedit /etc/X11/xorg.conf
and adding Option "AccelMethod" "UXA" to the Device section of your xorg.conf
** Changed in: compiz (Ubuntu)
Status: New => Invalid
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Jerky flash full screen videos in firefox
https://bugs.launchpad.net/bugs/334072
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