Sounds to me like it's Band-in-a-Box regenerating the song when you press play. This is what Band-in-a-Box does when you press the "Play" button. I would suggest pressing the 're-play' button instead of the play button. But once you close the program and save the song it will regenerate the ending next time you open the song again.

Try editing the notes on the melody track only. If you edit the notes on the instrument tracks it will regenerate when you press play.

Dave