Just because you have chords in the bars doesn't mean the selected audio track has audio in those bars. Instead of manually setting the from-thru go to the 'fancy' Tracks window, right click the track and 'select whole'. Or if you want to do it from the old window, use the 'Tracks' pulldown menu at top and choose 'select whole' (after selecting the audio track you are generating harmony for). This will highlite the track only where there is data.


I do not work here, but the benefits are still awesome
Make your sound your own!