So Windows sees the drives enough that it assigns drive letters, and device manager sees the drives which means they are being recognized by the computer bios. This seems to indicate to me a Windows problem, but I'm not sure how to help with that.

This is a long shot based on something I read some time ago. Is there any chance you un-installed anything like anti-virus software? Without searching, I can't remember which brand it was, but I distinctly remember some software that could disable the drives if not handled correctly.

Just to be sure, though, I'd be testing at least one of the drives in another computer before I spent much more time on this system.