I would like to say first off that you won't see any difference in performance from 4x to 16x with a 8800GT. That being said I know you want everything out of your system that you paid for and it bothers you that it's not working the way it should.
I really can't see anything except maybe a BIOS setting that would limit one of the slots to 4x. I would say to do a CMOS reset and that might help to straighten things out. Also check your BIOS version and look at the XFX message boards to see if others might have had this problem. You could also try pulling the cards out and blow some compressed air in the slots and then re-seat them and see if you're still having the same issue.