I've just started playing far cry 3'and I'm noticing a very strange frame rate issue. Quite often it will appear that the game is dropping frames when fraps and precision are reporting a solid 60fps. It will stutter for a second or so then go back to normal but this happens quite frequently. The only time I notice actual frame rate drops is during firefights. I'm running the game pretty much everything maxed except water and aa and vsync on. Any thoughts as to what could be causing these odd stutters?
1) I missed the fact you had SLI so your performance should be better than I thought. I also found someone stating they could improve performance in SLI but I can't test that myself. This fix may not even apply now though. I'd be surprised if NVidia hadn't sorted that out in their drivers.
I also suggest you try disabling SLI and run on a single card to see if that works better for you. Your frame rate would drop, but it may be smoother. Also, the above link refers to the GTX780 but it seems to apply to other AMD and NVidia cards.
3) Adaptive VSYNC:
I suggest you also try this. If you're over 60FPS then VSYNC will be on, however it will be automatically turned off below 60FPS. This may help certain types of stutter. FRAPS reports an average so it may not register really quick drops but those might register visually.
Adaptive VSync is forced on (should be done per game, not globally) through the NVidia Control Panel under "Manage 3D settings"; if you recently launched the game, just click "ADD" and then add the link that appears. That's easier then hunting down the EXE file manually.