I'm putting this in "General" because it doesn't SEEM to be a driver or configuration issue. My wife has a Dell Optiplex 745, Windows XP-Pro 32 bit SP 3 installed. We've JUST gotten rid of the malware known as "Norton Go-Back" on her system and it is seeing the primary HDD fine. Windows will NOT recognize an identical drive to the primary (10 digits difference in the serial number) attached to SATA port 1.
Bios - Sees both HDD perfectly
Ubuntu 12.0.4 Live CD - Sees both drives just fine. Along with all of the files on the secondary.
Data hasn't been lost, she just can't GET to it within Windoze.