Let me ask you something.
You pressed (or didn't) the "scan for hardware changes" tab in device manager and it did not install the "missing" display adapter ?
Did you see any hidden display device in device manager ?
Does windows install automatically gpu drivers through windows update (make sure that it does not)
Did you reboot ?
Have you tried clean uninstall-install drivers as stumped has described in detail in the sticky thread ?
gigabyte X58A-UD3R rev.2, core i7 975 3.9ghz (stock voltage), windows 8.1 64-bit, corsair 12gb DDR3 1600mhz 7-7-7-20 RAM, sapphire HD 6990 (stock clocks), coolermaster ultimate 900w PSU.
amd catalyst 14.6 RC2 june23