Glad that you could identify and fix the problem.
> Now, my challenge is how to retain the numbering and indexing of
> these scores in the document without treating them as figures. I
> want to be able to cross-reference the scores within the text and
> have them appear in the table of contents under their respective
> section.
This is a LaTeX question. The standard mechanism is to use `\label`
and `\ref` (or `\pageref`) for cross-references. Similar commands
exist (for example, `\addcontentsline`) to add entries to the table of
contents. Just add such comments right before a LilyPond environment.
Werner
