Do you have something else in the other PCI-E 16x slot? Your board supports running one of them at 16x mode, or both of them at 8x so if the other slot is empty go check in BIOS to make sure its not looking to run two cards and automatically splitting the lanes.
It says that the slots work in X8 mode regardless of single or dual card configuration. Weird, I have never seen a motherboard like this before. It has 16 lanes, but it seems that 8 of them are hardwired to one slot and 8 to the other, it can't allocate all 16 lanes to one slot.
It says much the same thing in the manual I downloaded from ASUS.
I wouldn't worry about it too much as HardOCP just did an article showing that SLI and CrossFire are not handicapped by running X8/X8 versus X16/X16. If running X8 on two cards doesn't bottleneck performance, X8 on a single card shouldn't be an issue.
Well that's dumb. Why bother telling me it runs at x16 then turn around and say it doesn't.
But apparently it "handles" pci-e x16 cards, but runs them at x8. So whatever.
Anyway, it's good to know that I wouldn't really notice any difference from x16 to x8.
I do play a lot of Bad Company 2, so I was hoping if I did get x16 that it would be a huge performance increase, but now that I know that I can't change it to x16, I'm glad there isn't much of a difference.
Thanks a bunch techgeek, now I don't have to worry about it anymore.