What card and what driver version?
I've found that for SH4
no driver above version 10.9 works very well with at least the 5970...
It *may* have to with your AA-mode. MSAA is known to cause problems, so try AMSA or SSAA. Is A.I disabled? Not good!
Try a CCC reset as click on Defaults...
Or do as I did. Crash the system
and make a restore!!
Still don't understand what happened back then, but it's been working fine ever since...