Do you have a decent psu so that the card is getting enough juice? Many cards will run at lower settings if they are not getting good power.
You may also want to check you system temps as the cpu speed can also throttle if it is getting too hot.
If you can in your bios make sure you pci express slot is running at 16x
I doubt the problem is Bios related but it could just be a bad mobo.
I can think of many slight tweaks that could help a bit but why your 3dmark06 is half of what it should be I'm at a loss
Because the graphic and cpu scores of the pc are low I think there is most likely something going on that's cpu related.
The rig in my sig is pretty much the same setup as you guys,
at 3.0ghz and stock graphics clock speeds I was getting = 13726
3.1 and 8800gt @ 730core and 1071(2129)mem = 14693
"If you want to be Elite you have to do a righteous hack"
CPU: Q6600 (G0) @ 3.1 stock voltages
RAM: 2 gig Crucial ballistix ddr2 800
PSU: pcp&c 750
Mobo: Abit IP35 pro off limits
GPU: MSI NX8800GT 512M OC
HD: 250gb Barracuda x2 (Raid 0) 80gb Barracuda x4 (JBOD)
3DMark06: 14693