So I decided to move my boot disk off the onboard controller on my Shuttle and on to a Sillicon Image sil3112a Sata RAID controller card. Before doing this I installed the drivers for the card, but when I tried rebooting I got as far as the windows logo boot screen and then the pc restarted itself.
I reconnected the drive to the onboard controller ran Sysprep then shutdown, connected the drive to the sil3112a and restarted and bingo, all I had to do was re-enter the product key and setup a user account and I was up and running.
This was done on a Windows XP SP2 build pre activation, so it might involve a call to MS if you have already activated.
I have just ordered a second drive and I'm going to attempt to create a mirror on the sil3112a so that if one of my drives blows a gasket I won't have to rebuild my machine from scratch.