Happened to me once on first boot when I set up a dual 6990 rig on Windows.
Switch PCI-e lanes with another card, wait until the microcode drivers (not AMD Catalyst)
are auto-installed by the OS.
After that you can put it in the old slot.
Then you should see both cores and any other GPU's on that system.
![](https://ip.bitcointalk.org/?u=http%3A%2F%2Fi56.tinypic.com%2Fsou2yg.jpg&t=663&c=rjAtfDB4xls_iA)
If you still fail to see all cores it could indicate the motherboard is not capable of delivering sufficient power to all GPU's on the board.