If you remove all of your cards except whatever you're using for video (the one in the primary x16 slot) and ONE additional card in the x1 slot via a riser, what happens?

If the card on the x1 slot still does not work, and you are certain that both the card and the riser are working, then you may want to try shorting the A1 and B17 pins on the motherboard. Most recent motherboards have not needed this trick, but if you look around on the forums, there's a couple of old threads about this. I had an Asrock N68S-UCC board that required it in order for the x1 slot to be used with a riser.