So I have installed W7 64Bit Ultimate as of recent, I have had SLI for some time now - 2xGTX260's (tho with my prev. OS - Win XP Pro I have never tried running Crysis in SLI).
All the games work perfect with SLI except Crysis (decided to try it for its DX10 beauty). What I get is basically strange periodic freezing in the main menu - music keeps playing, but mouse would stop moving for about 5 - 10 sec and then would resume, and this happens every 10 seconds or so - so its unmanageable. I am pretty certain this is the driver issue (196.21), at least i think it is. When i force it to run with a single card - i have no issues.
I'm experiencing a similar problem with 2 8800GT's in SLI. I've found that running the game in a window resolves the issue. When I boot up the game proper from a save file, I can then change to fullscreen without any problems. The issue only occurs in SLI, and seems to coincide with the installation of the 196.21 drivers.
I do, however, experiencing periodic freezing during gameplay, but I think that's a separate issue.
Did you by chance add another periferal, or change your mouse or keyboard out for one that is wireless or backlit?
I had your exact problem a couple weeks ago, and it turned out the new keyboard I bought drew too much power, and as a result it would get uninstalled by windows. I also had the same issue when using a KVM switch with just my mouse (sidewinder x8). The mouse would uninstall, making it not work for 5-10 seconds, then it would be recognized by windows again, and reinstall.
I eventually found that my keyboard, which draw too much power, had to go. I replaced it with my older keyboard and all issues stopped.
This problem only happened in one game routinely, due to the extra strain the game put on my machine, which could explain why it only happens in crysis.