I know what you mean about sometimes a stray chord creeps into a generation that can interrupt the flow of the progression. Because I always take my tracks to a DAW and dress them up there, this is not something that bothers me. That said, though, if BIAB is used in a live setting, which many people do, it would be much better that the progression is kept as smooth as possible.
Program settings which are worth investigating and which might help obtain smoother chord progressions are found under "Song Settings". For those who read this and don't know what I mean, this is found by right clicking on the chord sheet and selecting "Song Settings" from the menu that pops up.
I've labelled the relevant settings on the image below.
'Force...simple arrangement' (#1) can be effective as it reduces BIAB's decision making when choosing chords.
'Ignore slash root...' (#2) can help but only applies if you have chords such as G/F# (which is saying 'G chord played with an F# bass).
'Avoid transposition...' (#2) is one that I nearly always use. Having this selected reduces BIAB's freewill and forces it to look for exact chords and not 'close' chords that are then transposed with elastique.
'Natural arrangement' (#2) is new to BIAB 2017. By selecting this option, BIAB's decision making is increased such that it looks for ways to create the best sounding chord progression.
I don't know how these options will work with the tracks you mention but they are worth experimenting with.
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