Hmm, well let's be sure we're talking about the same things. Starting with 2.5, the TD has two windows, which will be referred to as the Game window, which shows the Tournament screen, the Player Rankings, etc; and the Settings window, which obviously has all of the settings.
What do you mean by "the main program disappears"? Are you referring to the Game window? And if so, are you saying that when it switches from say, showing the Tournament screen to showing the Seating Chart screen, it moves or disappears?