My computer seems to work better with crossfire disabled. I know that some games do not support crossfire. But the games that do, still run worse with crossfire turned on. For instance, while playing BF3 on high settings with crossfire turned on I get around 26-30fps. On high settings with crossfire turned off i get aroun 50-60 fps.
AMD Phenom ii X6 1100t
Asus M5 A99X EVO
Radeon HD 7770 x2
8GB DDR3 mem
Far too often there are problems like this with crossfire, which is why i never recommend it. You could try using driversweeper to remove all traces of drivers, and reinstall the latest beta driver. I would recommend if you cant get it sorted, selling both the cards, and buying a single faster card.