Firstly all my references are to do with SATA drives and I am unsure if the problem is present for PATA configs, but i would still disconnect the PATA drives when I reference to disconnect SATA drives.
The Problem:
When doing a fresh instal of vista on a raid configuration with other hard disk drives present the boot files get loaded onto the first non raid drive (most cases drive d: ). Upon the first restart/reboot you will get an error 'BOOT DISK FAILURE, INSERT SYSTEM DISK AND HIT ENTER'
You can still access your fresh vista install by inserting your installation DVD and hit enter.
NOTE: do not press any key to load the boot dvd, just let it run by and it will automatically bring up your install.
A FRESH INSTALL IS REQUIRED TO FIX...