Did you set the PCI's to Gen-2? Two locations in that bios...
Don't worry about that PCI error in the device manager. Both of my Asus Prime Z270's show the same thing but both rigs mine fine (one nvidia rig and one amd rig).
I did not. Will try that. My other rig is running 6 1080Ti-s with same mobo with no problems whatsoever and did not set bios to Gen2