So, if anyone else is having this problem, I managed to get it running by doing the following:
1.) swapped the cards (put graphics card 1 where card 2 was and 2 where 1 was).
2.) Removed the CMOS battery to clear CMOS (apparently the button doesn't clear all of the settings)
After doing this at the same time and reconfiguring BIOS on the next boot it works fine! Not sure which did the trick, but because you have to remove the graphics card on the Z68 board to get to the CMOS battery I just did them both at once.
Hope this helps if anyone else has this problem.