Have you troubleshooted to make sure its not the cables; ie switching the working cables/card combinations around to eliminate that variable?
next, i would see if when you remove the working 2 if the others get detected.
my pic-e 16x risers work fine by themselves, but my mobo makes me jump the pci-e 1x hooked up to a card with a wire to force the auto detection of a card or something...
anyways, other people will likely wanna know the specifics of your machine before they can troubleshoot anymore.
I second this, did you get your auto detection wire in place ?
I'm not using the x1 port.
Switched the wires, it seems like it's the card's problem. Weird, hadn't have any problems until today. Hope I didn't damage any resistors.
[Edit: Now Ubuntu hangs on the purple loading screen indefinitely.]