I had the same problem few days ago. Setup was : 4 cards (5870s) on mobo, all with extender (16x and 1x). Ubuntu won't boot with a card on extender (Xorg failing) but will finally without. I had no issue in BIOS however.
The solution in my case was to directly connect the card with the (faulty?) extender on the mobo, leave the others with extender. (Actually, 2 cards up, 2 cards down on mobo, more space means also more vent)
I'm very curious about what caused that weird crash, if anyone got a clue...