MS-Windows 2000, XP et al do not call the DOS batch file Autoexec.bat at boot time, instead it calls Autoexec.nt when needed. What you need to ( as I have done on many occasions ) is to edit your old Autoexec.bat file, copy the entire contents and then edit Autoexec.nt which normally resides in \Windows\System32 and paste the clipboard at the end of it, don't forget to Save it.
Now when you call a DOS based programme, Autoexec.nt will be called setting all the run-time parameters as needed.
You may also need to do a similer excercise on Config.sys / Config.nt and do some experimentation to get your progs running OK.