9600GS in SLI?? If you meant 9600 in Crossfire, thats obviously not happening. So I assume you mean 7600 or 6800GS in SLI??
Anywho. Some games actually see a preformance hit when SLI is enabled.
So depending on the game/app, you might want to disable your second card.
The other suggestion, would be to make sure you dont have any older drivers (namely from another manufactorer) that are creeping about. Run driver cleaner and then post back your results.