Did you ever find a solution to the problem you described in your first post?
FWIW, I’ve been having the EXACT same problem with very similar hardware / OS:
Intel DX38BT mobo (X38/ICH9R mobo)
Vista Ultimate SP1 x64
Two identical Plextor PX-810SA drives (known to be rebadged Pioneer DVR-212s)
Probably unrelated but I also have:
eVGA Geforce 8800 GTX
1 x Raptor 150 drive
Creative X-Fi Fatality
Silverstone Temjin TJ-10SW
My problem is exactly as you describe.
Using different SATA ports, different chipset INFs, different SATA cables, swapping between the two identical drives - none help.
Once I did swap one of hte PX-810SA drives out for a Plextor PX-755SA. It stopped the disappearing drive, but the system would poll the drive every few seconds cauing the PX-755SA to make a clicking sound and the activity light to illuminate for a brief moment.
So anyway, if you did find a fix, or even just a thought as to the cause, I would REALLY enjoy hearing from you!