So after I ran the utilities Smart PC Care on Windows it needed to restart to finish fixing the registeries, and the computer got caught in a restart loop to Windows install dvd. I zapped the PRAM a couple of times to try and reset the startup disc, but that didn’t work, so i also reset the SMC, buy that didn’t work so I had to open the computer to eject the dvd from the tray and then the computer wouldn’t start at all.
Eventually i reseated all the hard drives and swapped out my PC GTX 670 for my GTX 270 and that managed to boot into OSX, and I set it as the startup disc.
Windows is going in Automatic Repair again, and will likely fail, wonder if the MBR thing will work?