"What I am missing is what would cause this situatuion."

1. Power spike/fluctuation/blackout/brownout while system was doing maintenance. This might cause corrupted files somewhere in DOS--maybe in "maintenance" files.
2. Someone deleted some "maintenance" files in DOS when they were editing.
3. Someone changed or deleted batch files when editing.
My guess is number one. If you can't start the scandisk.exe from the DOS prompt---then that file is probably shot---you'll have to do a copy from the CDs or DOS disk that came with the system.