There are two global variables compeating. One is DefaultMenu, the other is ACTIVE_MAIN.
DefaultMenu global comes from the factory set to "MAIN", and there appears to be no way to set it to anything else except by hand. There are no dialogs that set global DefaultMenu.
ACTIVE_MENU is the global set by Menus.s^MenuEditor. Once it’s set that’s your new main menu for the rest of the session. But when you restart Multi-Edit it uses DefaultMenu again for the main menu.