How does a ssd keep his computer from bottlenecking? If the cpu is not strong enough to run both gpus at full speed it still won't cause the issue dfk described.
@dfk. Do you use a greenpower hdd? Many of the new 1tb disks are greenpower 5400rpm disks that's used for saving power. They're not the ideal hdd for gaming and having your OS on. They also go into a sleep mode a while after being inactive and results in a 3-4 seconds freeze when the disk starts up again.
Also, could you specify what motherboard you have?
@Smoogles. You will not get temperatures under 60c with the 6990 on a reference cooler.
He will most likely have temps around 85-90c.