I am having the same problem.
I have:
x2 6000+ processor

MSI motherboard k9a platinum

8800gt

2 gigs ddr2 800mhz

vista home premium 32

My scores for 2.0 and 3.0 are both at about 2500 and that can't possibly be right. The scores should be double that for this card.

My problem my not be this but a lot of people are having problems with PCI-E defaulting to x1. Go to your nvidia control panel, click the help button, choose system information and see if your PCI-E bus says 16 or 1. If it says 1 then go into bios and change it to 16. If it keeps defaulting to 1 then I think you have to change bios.