I couldn't get the 2 16 slots working in a 16/16 and have my soundblaster in.
After the trouble I had with 2 GPU's and a soundcard I pray for your soul I really do. lol
The only setting I'm aware of that relates to the 8_4 slot and M2 is in the Advanced settings where you can switch it between the PCI slot or the M2, usually its on Auto and 'should' disable the m.2 slot when 8_4 is occupied.
They only other thing I can remember is you can set the PCI generation for each slot manually, in system agent I think it is (so much stuff in this bios I forget.) though it 'should' (I use comas a lot with this board) auto detect unless set manually.
What does it say in GPU post when you have all cards in?
Other than that make sure your cards backside of the slot haven't flipped up out of the pci slot when you screwed them down.
I go along with that. Try re-seating the GPU in the last slot. When I added another GPU in and even though it felt solid, it still wasn't quite in the slot as I thought it would be. In the BIOS, shows up as nothing and after making sure it's in, came up.