GA-MA78G-DS3H cpu header is dead?

Hello forum
I am putting together a system
GA-MA78G-DS3H mobo, rev 1, bios f2
amd 64x2 5400 black edition
ocz ddr2 800 reaper ed. 4 gig
ocz vendetta 2 cooler
antec sonata III 500 with included 500w psu
my problem:
the 4-pin cpu fan header is dead, so is the 4-pin system fan header right next to it. I tried the cooler fan in another system, it works.
tried switching to antec 430w psu, same problem, the cpu cooler wont start.
the only way the cooler fan will start if I plug it into a system fan header with 3 pins.
the mobo beeps short but continuous, checked the manual, it says possibly cpu, psu or socket is bad
I check, the cpu and heatsink are seated properly. I used the hex head philip bolts as suggested by another user on Newegg review.
So right now, I am at a loss. By hooking the cooler fan to the 3 pin system fan header on the side, i can boot, can get into bios ok.
Any suggestions to revive the cpu fan header? I sent an email to gigabyte support already. Hope that i can fix this problem without sending it back to newegg. Will a bios flash solve the problem?