With a 7990 There is no option for disabling crossfire. For all intents and purposes it is a single card; That is how CCC sees it. GTA4 is a horribly bad optimized game, but as for bf3, it should be fine. Start by updating the drivers, and if that doesnt fix it, try the card in another PC or a friends pc if you have that option.
If you cant get it to work and its a newly purchased card, maybe consider exchanging it