You may want to look into the A1-B17 pin shorting that was necessary on a good handful of older motherboards.
Back around 2012, I had an ASROCK n68s-UCC motherboard that needed it in order for the x1 slot to be used with a riser.
Found a decent reference thread:
https://bitcointalksearch.org/topic/list-of-motherboard-that-require-shorting-pin-a1-b17-for-pci-e-1x-to-work-36061
I'll try however the x1's used to work perfectly..
pics from months ago:
I don't know what happened, maybe I've burned both x1 slots?
If the x1 slots used to work fine without an A1-B17 connection, then I don't think shorting them will solve your dilemma.
What has changed since they were working?