Vista: Are there issues with the disk ID?

If the drive boots ok on its own with no errors then it is not an MBR issue and unlikely to be any boot files problem. The favourite has to be the bios boot order. Most motherboards now have three boot device menus in the BIOS. One that lists what device is connected to which channel. One where you can set what type of device is chosen first – CD, floppy, hard drive etc. Then there is a third that lists which hard drive will be accessed first. Are you setting this one correctly, and after every time you move drives around? On most newer boards this third list will auto adapt to what is found to be connected. Remove the drive that was no 1 and reboot and the next drive becomes no 1 in the list. Reconnect the old no 1 and it will not retake its original position, you have to do it manually.

I don’t know about your board but I would be surprised if it did not have a boot menu that you can access by pressing a function key at bootup – possibly F12, but it should tell you at the bottom of the first POST screen. Have you tried booting the drive with that and does this fix the problem?