I can confirm I got the same problem.. I could not understand why my mining income suddenly had halved, and now see why.. It looks as if both cards are working from the setup, but like OP explains I can only turn on/off one of the cards - trying to turn on/off the bottom card will only toggle the top card - and I know from my other rig with 1 card that the Hashrate I get is equal, before it was double as this RIG has two cards.. disabling one card gives the same rate.

I'll try to revert to an older version of NiceHash Miner as it's no good only getting one card to work.