Well it sounds like to me, if it worked fine for awhile before, and now its having some issues... I would rule out the software. Uninstall the nvidia drivers motherboard drivers, and install the latest and test, Nothing lasts forever. If its still happening then one card could be bad. Test 1 card, and play a game on low settings or medium perhaps, Whatever you feel. If the tests are successful with one card, then remove, and place in the other and test. Process of elimination. If they work fine individually with no speed issues. Then you know the cards are ok.
Last step - Reinstall the OS, fresh updates, installs, reinstalled games with SLI enabled etc... And test.
Best guess. OS, or 1 card is failing, Way out to lunch, the board could be going if temps are good.