I've noticed that as well, though I haven't burnt the files to a DVD yet. I tried playing it in VLC and it would always skip the menu and go straight into the 1991 soundtrack. If you let the film finish, it'll dump you back into the submenu for the 1991 version, but none of the buttons work, minus the go back to the main menu one. And even when you click on it, it just replays the film.
The VOB files are fine, it's just the menus that don't work. I think it's possible just to re-create the menus without re-encoding the whole DVD.