Ok I solved the problem, what I had to do is put the drive into it's own raid array and now it works fine. I'd imagine that I had to do this because my original raid array was set to be bootable, and even though my raid controller was disabled it might have been confusing things somewhat, well...
I recently purchased a 500gb Seagate barracuda hard drive (http://www.dabs.com/productview.aspx?QuickLinx=3W4M), I can format the drive and use it as normal, but as soon as I try to boot from the drive it fails, I normally get a 'non-system disk' error upon boot up after installing windows xp...