Just for completeness, I did get a reply from the LOC that helped clarify things. I believe it's just an condition of the single application firm. All is well.
.....

..Copyright response

....concerning the Single Application, if you composed and performed the music using the Band in the Box software solely as the “instrument” or voice, it is eligible for Single Application. But if the software itself created some of the musical content by using computer-generated means, or if it incorporates any pre-fab tracks or other software-generated content in the piece, then the work does not qualify for the Single Application.

The rules for Single Application apply to purely to the content of the deposit, even if you are the only author of the work, have sole rights to the work, etc.....(end quote)