Bill,
I do this all the time with midi files I have created from another software program, Music Time Deluxe. I always insert the song (MTD) with a two bar offset to account for the BB two bar lead in measures. Try this, if it doesn't work, then we probably need to look at your midi file and determine how it was created. All in all, the midi file measures need to line up with an exact replica of the measures you outlined or inputed into BB. That includes time signature changes and etc. Therefore you will want to offset the midi file so that measure one of the midi file lines up with measure one of the BB song. Hope this helps and I also hope I'm not being redundant.