Dave,
This is most unusual. BIAB only plays the chords it's been instructed to play. The song isn't frozen is it? Any track(s) that is frozen will not regenerate. If this is the case, unfreeze those tracks and then regenerate.
Something else to try ...
Right-click on the chord chart and then select "Song Settings". Now activate "Force song to simple arrangement". (That's the one above the "Tag" option I have highlighted below.)

Once the "Simple arrangement" has been activated, the song will need regenerating (unfreeze any tracks before doing this).
Hope this helps,
Noel