The proper way to clear the CMOS on ALL AMD Chiipset motherboards from GIGABYTE is to jumper the CL_CMOS pins (on the 990FXA-UD3 -
next to r the F_PANEL in the corner) WITH ALL POWER OFF. Count to 10 then remove the jumper and reboot. You should be back to factory settings.
I've used this numerous times on: 2 690, 2 780, 2 785, 1 790X, 4 880GA, 1 870A, 2 990FXA-UD5, and 2 990FXA-UD3 Boards that I am
currently using in my house and it has never failed to restore settings.