It turned out to be the riser cable after all. I had rebooted the VM and nvidia saw the card this time and lshw was showing it was using the nvidia driver. However, when I tried to run the bandwidth test against the second GPU, everything locked up and I had to do an ungraceful shutdown.
At that point I was sure either the GPU had a serious issue or the cable was bad. As soon as I swapped the cable out for a different Gen4 riser, everything worked perfectly for both 3090’s.