Update....

This issue was driving me absolutely nuts. Finally, I decided to contact tech support. They opened my midi file, and were able to re-create my problem. They will look into it.

Seems that BIAB does not map MIDI correctly in some instances. For example, I believe it trips, if there is a program change before the first note. It sees that program change as a "first" note and maps bars incorrectly. In any case, I am glad they acknowledged the issue and VERY hopeful they will fix this, as most of my midi things are/will have same characteristics.