Bhops123 :
UPDATE: I had the motherboard replaced, and it was fine and I now know for sure that it is the graphics cards alone. I tested the cards earlier today and both cards had equal temps during a furmark test, however when I just tested them the second gpu didn't rise in temp. At this point, I'm wondering if the cards are lemons because with me just getting my motherboard replaced, I know something is wrong with the gpus themselves.
Hold on. You are jumping to conclusions. What game were you playing that only used the 1 card? Not all games support SLI. If Furmark did, and the game didn't, chances are, the game doesn't support SLI. It also sounds as if you have a severe bottleneck, as even the card that is in use, is only being used to half its ability.
As I mentioned before, some of those games are severely CPU limited, and no matter how fast your GPU is, you can only go as fast as the CPU feeding it. And in at least 1 case, some games simply are coded poorly, and no matter what hardware you have, you simply will not get high FPS (Online Arma games for example).