I also have this problem. Works fine when visual effects are turned off.
Specs
8.10
Latest updates
ATI 4850 (single kernel) g-card
amd64
** Changed in: xorg (Ubuntu)
Status: Incomplete => New
** Attachment added: " lspci -vvnn"
http://launchpadlibrarian.net/20326847/%20lspci%20-vvnn
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All GL applications flicker when Compiz is being used
https://bugs.launchpad.net/bugs/228233
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