Your MBR is probably damaged. You may need to a write new autoexec.bat file to get to windows. Can you get into windows from the DOS prompt? If so, then this is the most likely cause of your problem.

If there is no Windows directory or windows does not start, I would look into a full reinstall. Something formatted your hard drive or Windows was too badly damaged.

In addition, make sure you are not shutting your computer down to 'restart in MSDOS mode' every time.

Hope this helps.