i'm a bit puzzled. the ACW figures out the tempo, key and chords. to do that you set bar 1 as one of the first steps. you set bar 1 so why move the audio? only thing i can think of is that the audio starts with a pick up bar so you have a 4/4 bar with a couple of beats of silence and that is what you have called bar 1. just start bar 1 on the first beat of the first full bar.

or have i misunderstood totally?