Just some elimination I would go through in your situation:
try one card at a time, ensure both are recognized by windows and are fully able to install drivers and run a 3d test on.
Next, (assuming both cards pass the last test) I would test both PCI slots. Looking for the same thing as before.
Next, (assuming the motherboard passes the last test) I would ensure that they are the same card. Sometimes people get a 2gb & a 4gb and don't know it and this sort of thing happens.
The cards have to be Identical architecturally to run sli... make sure they are.
other than that, I would start looking at playing "swap the video cards" with a friends rig if possible to see if it's the cards or the motherboard.
Added: If you cant tell if the cards are different or not and the are recognized by windows correctly, use GPUz to see if any differences exist. Open it twice like i've done here and select different cards in each window... and compare.
~MG~Edited by MadGoat - 3/28/14 at 8:57am