I purchased a ROG Strix X399-EGaming motherboard with a 2950x TR2, running BIOS 0801 recently. I had two flash drives in the M2_1 and M2_2 slots, running Windows 10 and LInux (Ubuntu 18.04). Either OS booted fine when set as the primary boot device, but the GRUB bootloader on Linux very often would not detect the second flash drive at boot (saw the drive just fine post-boot). Turning off Fast Boot solved my issue.

I believe this is a BIOS issue. Further testing showed that if I rebooted from the BIOS screen, the second M2 drive was always detected and booted Windows from GRUB. Any reboot initated from cold power-up or from the Linux OS, however, resulted in the second M2 drive not being seen by GRUB at boot, and only being detected once I had fully booted into Linux. I hope this helps someone else going the dual boot route.

Galael