I have had this problem in the past where it has been a faulty SATA controller. You have tried a fresh installation of Windows? Often only individual SATA ports go faulty and that by connecting the disappearing drives to another port can cure the problem.
I haven't tried fresh Windows yet. As far are using another port I cannot because I have 6 drives and only 6 ports.
Update: I was using the standard Windows AHCI driver so I updated that to my chipsets AMD AHCI driver, hopefully this will cure my issue.