It would be using whichever MDW file is pointed to in the shortcut, e.g. if the target in the shortcut is....
"C:\Program Files\Office97\Office\MSACCESS.EXE" "C:\Projects\AppDev.mdb" /wrkgrp "C:\Projects\MySystem.mdw"
.... it is using MySystem.mdw in the "C:\Projects" directory.
If "/wrkgrp" isn't specified, it would use the default System.mdw file.