Rests interfere with re-pitching
Take the sample score, start re-pitching the chords from the first measure using keyboard. It works very well, for example, you can do this smoothly: C, Shift+D, E, Shift+F, and the two chords in the first measure will be replaced. But for the second measure, after pressing C, Shift+D, you have to pass the rest (by typing a pitch or 0) before re-pitching the second chord. This only happens to chords (with more than one note), because only after re-pitching a chord does the blue (or green, ...) rectangle fall back.