that "some reason" is because your BIOS sets the order of drives to boot from, and yours is set to boot from the storage drive first, then the system drive. When you install windows, if it detects such a thing, then it will put redirecting boot files on the other drive.
In my experience they are not necessary as long as you change your bios to boot from the correct drive. But don't go deleting them just yet.
Perform the following test.
1. Turn off your system
2. Unplug the storage drive.
3. Turn on your system
With only one drive it should default as the first boot from drive, and if I am correct about the files not being necessary it should load windows without a problem.
If it simply loads vista:
1. Turn off computer
2. Plug the storage drive back in
3. Turn on computer
4. Delete the boot files from the storage drive.
5. No bios change is needed since it should have already adjusted when you had only one drive, however if your motherboard's bios is weird it might point at the storage drive again, in which case booting will fail. If that happens you need to go into bios and make sure the OS drive is set as first boot.
You might have to clean the MBR of the storage drive as well.
If it does NOT load vista:
1. then turn off your computer
2. Plug the storage drive back in
3. Turn on computer and go into bios right away
4. Change the boot order to boot from the storage drive first (so that it gets those boot files instead of failing to load with the ones from drive C).
I doubt the second scenario will occur or be needed, but I don't want to leave you without instructions on how to reverse the process in case it does go wrong.