Just completed a brand new build and this is driving me insane. I have the X99 FTW and I am trying to SLI 2 980 GTX SCs. I put in 8 sticks of 4GB DDR 4 RAM and I have the 5930 CPU. I tried the obvious slots 1 and 4 going for x16/x16. The BIOS only sees slot 4 and shows it to be 8x. I thought it was the 980 in slot 1 so I swapped them. Same thing, BIOS only sees slot 4 as 8x. Tried moving them around, tried forcing all slots to 2.0, made sure dip switches for all slots are on. For what it's worth I am using the SuperNOVA 1050 psu. I even tried connecting the AUX power, no luck. I totally don't get why the one slot it sees it sees as 8x. The 5930 should have plenty of lanes. I also tried several bios versions up to and including 1.16.
 
The only other BIOS settings I changed was to use the 2133 RAM profile, CPU multiplier to AUTO, SATA 1-6 to RAID (I have two velociraptors in RAID0). Windows 8 Pro boots fine, I just can't see the card in slot 1 so no SLI.
 
Any advice would be greatly appreciated. Thanks.

husseyka
I thought it was the 980 in slot 1 so I swapped them.

Since you already tries swapping get them, try resetting the cmos. Check in the bios at the top of the screen and see if it shows anything in there about which cards are installed.

I also suggest removing and reseating the cpu. Glance in and look at the pins to make sure nothing bent while you are reseating it.

Hopefully it isn't a bad lane, but if it is, EVGA is quick to help get it replaced.