What happens if you only have 1 card in the slot where 2nd GPU isn't detected? If no GPU is detected it likely is the slot.
If a single GPU works in multiple slots then it isn't the slot. Make sure the bracket (or GPU or case) isn't bent. I once had a card with slightly bent bracket. Just enough to prevent card from seating all the way.
No GPU is detected when only 1 card is in the "bad" slot and I get no video at all.
It's an open air rig so seating isn't a problem. I'm using extender cables and I've confirmed they both work.
Temporarily try plugging 1 card DIRECTLY into "bad" slot. If still nothing then I would be leaning towards bad slot.
If card works directly but not with extender then depending on the extender you may need to do the "short sense detect pins trick" (searching forum will find the thread).
