The playlist generator does not repeat tracks, if you have configured it properly. In your case it seems that the playlists are created, but not played yet. So when creating the next playlist, it looks at the tracks that are in the playlist window, waiting to be played. It checks only tracks after the playing track. And how many tracks - depends on the settings in the playlist generator: Settings tab, "Repeat protection considering tracks in the playlist" (must be enabled) and click the "..." button to set up how this works.