I noticed this quite some time ago when Vista was first released, it seems that if you use AHCI mode for your HDDs the boot info/files get put on a different HDD to the OS, strange, but true, then, if you want to remove the HDD that has the boot files on it, you're screwed, Windows won't boot.
What i started doing is installing Vista in standard IDE mode, when Vista was installed i would change the drivers within Windows for the AHCI drivers then set the HDDs to AHCI mode in the bios, this would overcome this issue.
Sorry i haven't been of much help, but, as rpstewart has said, the easiest way round this would be to reinstall Vista, also, install in standard IDE mode and then change the drivers manualy (forced) within Windows to the AHCI drivers, reboot and go strait into the bios and change to AHCI mode, this worked for me.
PS: You may need to format your Backup drive that is currently holding the boot files before you reinstall Vista, this is because you can't delete the boot files within Windows without a load of hassle.