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Do you have the Linux drivers for your display card loaded?
I've had the same problem with FC11 desktop effects with older Nvidia Linux driver versions. I've got a PCI-EX 7950GT, but after upgrading to newer driver versions some of my problems (much like yours) have gone away, while other artifacts have emerged...
I. e. the first step you may try to fix your problem is to upgrade to the newest driver for your display card.
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