Thanks!

I did some experimenting, and it does look like patterns are referenced to the most recent part marker. I can force the song to "reset" the reference point just by setting the measures to 'substyle a' where the two bar pattern is needed.

Also, changing the weight made no difference.

The song has an extra measure at the ends of some parts. Just when you expect the next part to start, you have one more measure yet. Sort of like the extra 2 beats that are often used in country and bluegrass, except these are 4 beats. Probably never would have noticed the problem if the song was different.