[SkookumPete]

I believe this is a related question. I am pulling the project into Calibre by pointing to an HTML file that references all the source files, in order. Some of these files have references to footnotes, which appear in the last file listed. However, when I convert to MOBI, what appears to be happening is that the first file in the list is brought in, then the footnotes file (because there is a footnote in Chapter 1), then all files referenced in the footnotes file (all notes being linked back to the text), then finally all files that do not have footnotes, in order.

So Calibre seems to be pulling in the files as they are needed to resolve references, rather than in the order listed in the pseudo-TOC file, and they appear in the text and the generated TOC in the wrong order.

P.S. I see now that this is "by design" and the option has to be changed in the HTML2ZIP plugin.