If you're running crossfire or sli both cards will run at x8 mode, whereas if you stick one card in lane 2(second from the top pci x1 lane) it says it should run at a full x16. Did you accidentally put it in lane 5?
As has been said by FuryRosewood, there will be no noticeable difference since even the very latest GPU's are not capable of using the full bandwidth of x16. Not by some margin infact.