What might have happened is that you created a new (primary) partition before the one windows boots from, effectively shuffling partitions and possibly bumping the win partition number - hence the boot.ini needs to be adjusted. If you can mount your windows partition RW (fat OK, NTFS through native), you can do this yourself. The easiest is probably to use the windows recovery console (google for this...), but if you have one of those stupid "restore system" CD's instead of the MS vanilla media, I am afraid this might not be available...