I'm seeing the 960 evo drives having weird compatibility issues on x99 boards.
2x asus X99-A II boards, updated to latest 1401 bios
2x Samsung 960 evo 500gb m.2 ssds
1x intel 600p 512gb m.2 ssd
1x gigabyte z170mx-gaming 5 board
All 3 m.2 ssds work great on the gigabyte, even with a heavy OC.
The intel 600p works perfectly on all 3 boards.
The Samsung ssds both display problems on both the asus x99 boards though. On a cold boot they recognize 75% of the time. On restart they recognize only 25% of the time.
Nothing plugged in to any other pcie ports, nothing in the u2 port, removed all peripherals down to kb/mouse only, and default settings (no oc or xmp, ddr4-3200 @ 2133) and nothing seems to help it. One of the power supplies is a evga 80+gold 650W and the other is a 1200W Corsair. Tried bios settings for hours, no dice.
I cannot for the life of me see anything other than a firmware/bios incompatibility being the cause.
OP is your board an X99-A or an X99-A II ?