>
> Especially oddly, running scribble with --latex and then manually making
> the PDF works, except that the table of contents is blank.
>
Check if it works when you make the PDF twice.
This sounds like it's trouble resolving cross references.
Maybe there's a bad character in a label [1], maybe
I have a document written in #lang scribble/manual that used
include-section to include a section written in #lang scribble/lp2. It
renders perfectly to HTML, and I can render both the literate program and
the main document, with the inclusion of the literate program commented
out, to PDF
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