I recently purchased two GTX 980s (ASUS) and just to be safe I uninstalled previous drivers (I had AMD before this, and just had to go back to NVidia) used a program to completely rid of display drivers. Then plugged in my two cards. It appears the one in the first slot works, and the second, no matter which slot (although preferably the third as its the second x16 slot), refuses to show up in the BIOS. I have the latest BIOS as well. I did everything I could find on other boards, such as not installing PHYSX drivers. I cleared the CMOS, updated drivers as much as I could. The BIOS simply cannot, see anything in the other slots. It is not the graphics card either as I've swapped them back and forth. Both work as the primary card. This is a $500 motherboard, it should definitely be able to pull this off, despite being newer cards. I doubt its a power issue either as I have a 1050w power supply.

I have tried getting in contact with ASUS tech support and they are being as helpful as they can, but still nothing.

In the mean time, one is working just fine.

Any one know of a way to check if PCI slots are bad? or if perhaps they are turned off? How to turn on?

I have them connected with an SLI bridge, and while the PC boots up both do light up, and fans begin running in both. Once windows boots up, however, the second card stops working.

Of course since the motherboard doesn't appear to be detecting the second card my OS certainly does not.

Thanks for any help anyone can give me.
i7-4930k @ 3.9 Ghz, Corsair H100 CPU Liquid Cooler, ASUS Rampage IV Black Edition, ASUS GTX 980x2 SLI, 16GB Corsair Ram, 1050w Corsair PSU

SOLVED.

I cannot believe I didn't think of this. There is a switch on my motherboard for each PCI slot and I simply had all of them except the first turned off.