Did you try swapping pcie slots? Sometimes you have to switch the order of installing the drivers like nvidia first then amd or amd first then nvidia. Although it tends to be the amd gpu that doesn't work. What gpus are they?
I kept the 1080 in the top slot but, I did try the r7 360 in two separate slots and swapped to my other default bios on my dual bios motherboard. The fan ramps up as soon as I power on and it's not recognized in device manager. Im certain the card isnt failing. I just took it out of my other machine last week. I've also had it working as the primary card in this machine before.
They can just be finicky about which slot. Weird bugs get weird solutions and you just have to try whatever to get them to work. It doesn't hurt to know it will work alone either.