Not clear on exactly WHAT operating system your father is using. The only DOS I remember that booted from CD was PC-DOS 7.0 (and later)...
To get into Windows 3.1, one simply typed 'WIN' at the DOS prompt (as you correctly recalled).
However, if he is in DOS and 'WIN' doesn't get him anywhere, check the PATH variable (type 'PATH' at a dos prompt) to make sure the windows directory where the WIN.EXE resides is shown.
I can't believe someone is still using DOS/Win3.1, though... that's .. uh... well, that's that.
If it's Win9x, then there are all kinds of other problems and solutions. Let us know a bit more on the details and we'll see if we can help.