I haven't uses ACW in a very long time but I seem to recall that you have to set the starting measure in it for it to line up.

another option is use a DAW that lets you click and drag the track on the time line so that you can get it to line up properly.

Every time I tried to use ACW.... most of the time it was fairly accurate with the chords in simple songs.... but it can get pretty far off course in it's guesses sometimes when the chords aren't simple triads or the bass note is not in the root. After spending several hours one time to get ACW to give me the right chords AND to get it in sync.... I gave up and started a new song.... inputting the chords manually and I was done in 20 minutes time. The biggest issue I have had in using ACW is the sync issue. Defining that all important starting point.

Like I said, I haven't used it in a very long time mostly because I don't do things that require it's services.

You can find my music at:
www.herbhartley.com
Add nothing that adds nothing to the music.
You can make excuses or you can make progress but not both.

The magic you are looking for is in the work you are avoiding.