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.
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.