I thought it might be a power issue but it wasn't. When I start both GPU's up they start fine then, when they hit about 60% usage the 2nd one gets "connection problems" and drops back to 0. This isn't a username/password issue.
How can you be so sure it is not a power problem?
How much power do you have dedicated to your 6990s? What PSU are you using exactly?
The fact that the problems start whenever the cards go over a certain use percentage almost tells me exactly that power is the real source of the problem. Your cards draw more electricity as they ramp up in terms of "usage percentage". ie when your card is using 100% usage you are probably pulling ~300 watts each and when you are down to 50% usage you could only be doing 150 watts.