Another possibility is: rename file c:\windows\system32\autoexec.ini to something else (e.g. change "ini" to "bak"), then try it again.
Not many programs use that 16-bit subsystem any more, which means that that file may have been created and used by the very program you're trying to reinstall. If the program needs it, it will create it - but keep the .BAK file as a backup, anyway, in case anything else happens.