This can happen if you select "Free Position" in the Button section of the Settings Pane, move folders around in the menu, and then click "Save as Favorite." If you then try to use the original theme in a new project, the buttons may not be positioned correctly because your custom button positions are saved in both the favorite and in the original theme when you save a theme as a favorite.
To avoid this, update to iDVD 5.0.1.