Could be a drivers issue. What version are you using?
I found with a few drivers released this year that when I overclock my two GTX260's I too lose FPS. I currently get best results in ALL games with stock settings. If I overclock with my current drivers most of my games perform really well, but my fav two (Crysis and GTA4) actually lose 5 or so FPS.
The reason I don't change my drivers is because my current version allows PERFECT SLI performance in GTA4 where as most cause shadow errors and horrid jerking.