Re: X299 Dark Problems seeing second M.2 Drive
I wanted to chime in here and say I've been having a very similar issue on my X299 DARK and a pair of Samsung M2 SSD's.
I went with with a Samsung 960 PRO 512GB and a Samsung 860 EVO 1TB.
I put the 960 PRO in the primary slot (the one that can accept a 110 mm M2 slot, marked as "PM1") with the 860 EVO in the secondary (vertical, marked "PM2") slot.
EVGA 1080 Kingpin in the top PCI slot, and nothing else on the board.
Upon first boot, BIOS recognized the 960 PRO only (did not see the 860 EVO in BIOS anywhere). Windows installed just fine to the 960. I installed the BIOS update to v1.11 and did not see the 860 EVO. I installed the Samsung Magician, and it sees the 960 PRO but NOT the 860 EVO.
So I figured it was a slot problem. I swapped the slots (Putting the PRO in M2 and the EVO in M1). Nothing changed, it did not recognize the 860 EVO and the 960 PRO booted just fine.
I swapped them back, and nothing changed.
I haven't been mucking around much with the bios settings, so everything should be pretty much stock for the v1.11 bios update.
I've set up an RMA with NewEgg to see if it was just a bad 860EVO, but it looks like something else might be a factor than just a DOA SSD.