Have you tried twice as many 3/4 bars instead?
The Bars/Chords may cooperate better that way.

BiaB is based on 3/4 or 4/4 in my experience, and anything else is the application trying to adapt the the task (faking it to the best of it's ability)
So giving it 2X as many 3/4 bars may give you better chord control
Just an idea at this point

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