I'm running Xubuntu (linux) and as mentioned before I installed the drivers via the public repos. If I'm only mining on one GPU with two OpenCL instances then wouldn't that be a configuration issue in cgminer and not my driver?
Fine, don't believe the person who wrote the application 
Aha, well like I mentioned check each card on it's own to see that cgminer does read them each correctly in both PCI-E slots, and then you can confirm whether it is cgminer or not.