Could be a few things going on?
First, it could just be a bug in cpu/gpu-z. If you want to find out run 3DMark, then switch slots and run it again. If the results are the same in either slot, then it's probably just the bug they're talking about here and you can ignore cpu/gpu-z: DK 790FXB-M2RSH - pcie @ x4 instead of x16 - DFI Club Global Support Forum
It could be your bios getting twitchy on you... it certainly wouldn't be the first time I've seen a DFI bios spit out crazy random settings. See if there's an update for you: DFI LANParty:The Best OC Platform! Overclock, Motherboard, Intel, AMD
. As you're probably well aware, it's no small task setting up a DFI bios properly.
Lastly, that slot could be bad... but unless you're going to go SLI it's not going to impact you as you have a spare.