Kind of sounds like you need SATA HDD drivers to add using F6 key during Windows install, in order to successfully reinstall Windows. In fact, maybe that is what corrupted during your upgrades (not certain though). This would explain why you can see and access everything when the drive is hooked up as an external drive on another system.
Check your manufacturer's website for a SATA driver for your Hard Disk. If they have one, you should be able to use it to add to Windows while performing a Repair Install with your installation CD.
Check for the driver first and then let me know!