I have now upgraded my Ubuntu to 9.04 and the problem stopped. 
Before I upgraded I used fglrx. I'm not sure what video driver I am using now, 
but it's not fglrx.
lspci reports my graphic card as:
01:00.0 VGA compatible controller: ATI Technologies Inc M56GL [Mobility FireGL 
V5200]

since the problem is gone I'm leaving the issue as closed. Thanks for
caring =)

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gnobots2 causes Xorg to use increasing amounts of cpu
https://bugs.launchpad.net/bugs/375222
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