You may need to adjust the boot sequence in your BIOS first.
The problem might occur because Windows wants to load to the Active drive or the first drive in your boot sequence. I had just such a problem recently and my system wnated to load to my IDE master as opposed to my SATA. To check for this, load your setup disk and reboot. If Vista loads, this could be the problem. There are a number of ways to correct this. I took the thorough root and reloaded the system AFTER I changed the boot sequence to SATA master. You can create a boot disk, which will release all your files for imaging and then clone the system either on to the appropriate drive or the drive that you are currently using. Sysprep (not sure if available in Vista ultimate) is a fantastic tool to this end. Right click your computer and then 'manage' to have a look at your disk arrangement. This can tell you alot about what is going on too. This is my first post on How-To-Geek so please forgive my shortcomings and/or if I am talking down to you. Cheers, Nutcracker
PS those who know have been saved!