Ran into something vaguely similar once with restarting in MS dos mode - seems at some point it backed up the DOS boot autoexec.bat over the backup for getting it back into Windows Boot mode. I was able to repair the thing, but then, it was merely Windows 98.
A suggestion (for next time, unfortunately):
1) Get a CD-R(or CD-RW, DVD-R, DVD-RW), separate from a CD-ROM (or DVD-ROM) drive.
2) Get (or download/burn) a live Linux CD/DVD - bootable CD/DVD that won't try to install onto the hard disk (such as
Knoppix) (DVD works too, but they are more fragile)
3) Make multiple copies of the Live Linux CD/DVD
4) Double-check to make certain your machine will boot from a CD/DVD drive (and test it with the Live Linux CD/DVD).
5) Next time this happens, boot up with the Linux CD, and burn everything you want to keep to CD before reinstalling the OS.