Since the 'assumption' word has been thrown out already, can we assume that you have checked the appropriate boxes in song settings to not embellish chords, have adjusted the setting in the Arrange dialog dealing with allowing late notes X% of the time (X being between 0 and 100) and set your overrides to Force to simple arrangements? These options may or may not help with your specific problem, but they can impact the final output of BIAB considerably.

Good luck and I hope you find an answer to your dilemma.