Alright, so i'm fairly sure that there is actually something wrong with the 6990s themselves, even though they are both brand new.

I installed Windows from my alienware disk and experienced the same problem. I installed windows on my corsair SSD on the intel SATA controller (ICH10R), same problem. I went down the road to Austin Computers in Rockingham and picked up a Sapphire Radeon HD 5450 for $55 and it worked fine, with drivers installed (both the ones on the disk and the latest 11.8 drivers from ATI AMD website).

So I have drained my loop, taken the 6990's out, and intend to replace the stock air coolers, then see if I can get somebody to plug them in to a different computer and test them, just in case the problem has to do with my power supply or some other hardware conflict that would affect a 6990 but not the 5450. Then I guess I try either two new 6990's or a couple 590s. I'm not keen on having more than two physical cards on the computer, eg 3x 580s.

I'll post back if and when I am able to determine if the cards work in another system.