Wow, fast response - kovidgoyal!
OK, I reread the quick little blurb about the chapter regex from the help, and came to a realization of what the problem was.
The chapter regex only looks for matches inside a <H1> or other H tag, so since these were not inside H tags, they weren't found.
What I had to do was use another program (just whipped up a quick c# app) to wrap the matches in H1 tags, and save a copy of the file with the new tags, than re-ran the cmd line utility, and all was well.
Do you think it would be possible to optionally remove the requirement for the chapter regex match to look for the H tags, and just use the supplied regular expression to find the chapter headings?
Thanks