"I've had trouble when the pickup notes are not a full bar--i.e. 3 eighth notes in a 4 beat bar. My simplistic workaround is just to use a full bar and fill in rests before the pickup notes"

Or, you can import the midi, disregarding the pick up notes, and use the first measure of the midi file as measure one, and then, add the pick-up notes to the 2nd lead in measure (i.e. 1/2 Rest + 1/8 Rest + (3) 1/8 notes), through the BB music edit program so that your song starts on measure 1 and you still hear the pick-up notes.