Does the motherboard vendor have a driver for disk controller? On the "advanced" items menu during the disk prep you can add one via usb drive, floppy, etc. But I doubt that's it.
Likely something happened to the drive and windows attempted to repair it, but failed and left you with a corrupted drive. (I'm guessing this is the case since you mentioned that the controller and partition numbers are wrong)
Also could just be a bad bootloader pointing to the wrong partition. Rather that write that all out, here is someone that did:
Recovering the Vista Bootloader from the DVD - NeoSmart Technologies Wiki