both PCI-e slots work, but second card gives no video

So first I will put in a little background. I have a GA-X38-DS4 and it caught on fire a few weeks ago (power controllers overheated and shorted out). I got a warranty replacement from Gigabyte (And also a new CPU because it fired my basically brand new q9450). Everything else "seems" to be working (all 4 sticks of RAM show up, no memtest yet though) (Both graphics cards work independently of each other).

Now I have gotten the system put back together and seemingly working with one glaring expection. I can't get any video out of the card that is in slot 2 if there is a card in slot 1. I've tried switching the cards and power connectors. Both cards function fine by themselves in slot 1 or in slot 2, but as soon as there is a second card in the mobo the second slot stops working.

Is this hardware or BIOS?? If its hardware is it the Graphics cards or the mobo?? (Graphics cards still have warranty on them so I can send them back one at a time if they're the problem)

Help please, and thanks in advance!!