Ok, what happened is that your autoexec.nt got corrupted.
What you need to do is find your i386 directory. It will either be in C:\i386, C:\windows\i386 or you will have to get it off your windows install cd.
Once you do, open up a cmd prompt (start -> run -> cmd).
Then type this.
expand c:\i386\autoexec.nt_ c:\windows\system32\autoexec.nt
Replace c:\i386 above with wherever your i386 folder is located.
You might get a similar problem right after you do this saying either command.com is not compatable. If you do type the same thing, but replace autoexec.nt_ with command.co_ and expand it to c:\windows\system32\command.com
The windows support page for this can be found here