hai,

i fishing in the dark but my failer by my older (x-99 m2 slot and pci-e expcard) system was

1/ setting from start drive sata or pci-e and when you did set windows new up

did you deleted partition and set new up?

did delete partition and format ssd when you set up and did this in uefi modus or leg modus

because this where i made the mistake and it sound a bit similair .

before i had it figuard it out

at first it worked and after a short while i got a lot problm's

also importand is one drive was not from the start gpt so it had a small mbr ,

second drive begin gpt en when i clean ssd1 problms started.

so setting up settings in bios are most important

if this has nothing to do with your question sorry for my comment