OS: Ubuntu 16.04
RAM: G.SKILL TridentZ 16GB (8GBx2) DDR4 3200MHz
Two GPUs work no matter how I connect them to motherboard, be it via risers or on 16x slots. If M.2 installed, only one GPU works.
I remember seeing notes on specific AM4 boards that use of the M.2 slot will sometimes disable one of the GPU slots.
I'm not sure if your board is one of those, but it seems like *ALL* of the AM4 boards with more than one PCI-E 3.0 slot "shares" lanes between the second slot and the M.2 connection.
For some reason MB makers seem to dedicate 16 of the 20 (for Ryzen) PCI-E lanes to the first GPU slot on ALL of the boards I've looked at, and have to share out the other 4 among everything else.
Any AM4 board I've looked at to date with 3 x 16-bit slots use PCI-E 2.0 from the chipset to run the 3'd slot, usually at x4 or "share" x4 with other stuff.