You should be able to reinstall Windows from the CD (if it's an install CD and not a restore CD) and it will ask you if you want to format the drive or not. Simply do NOT format it and it will leave all the files currently on the drive intact. You'll likely have to reinstall some programs, but all the data will still be there.
However, have you called Microsoft about this issue? It may be a common problem and they can help you through it without having to reinstall at all.