Try every slot, with both cards plugged in till the board reads the both cards at the same time. Other than that, maybe someone else with this board can chip in their thoughts.
Try another slot and see if it gets detected. There's always the remote chance the second card is dead. I ran into that 3 weeks ago - wasted 6 hours operating on the assumption that the PCIe GEN3 slots were acting up. It wasn't until I gave up and tried the card in my rig at home that I find out that the card was DOA.
Nope, I can get the card to work if I move it to different slots.
OK, here is a "key" to this image:
Red := I have been told the card will not work here. Have not tried.
Blue := Open slot, I have been told that it should work.
Green := The card is currently working.
So, I thought it might be an x4 or x16 issue... you think that matters?