If you use markdown you need to use txt instead of rtf. Still allows you to do formatting, etc, but it's a different way of doing it.
Page breaks aren't a part of markdown, but one nice thing about markdown is you can mix and match snippets of html which could include a page break.
For example, I've been working on a book using markdown text as my master source, and I just stick the following line in the text file where-ever I want a pagebreak:
<div style="page-break-before: always"></div>
If you follow through with that option you would also need to use text input with Calibre, and there is an option there to tell it to use the markdown syntax when converting the doc.
If you want to open a bug with that book but you are worried about copyright issues just delete the majority of the content from each chapter, as long as the problem is reproducable I can take a look at it. I suspect it's because you're formatting the chapter headings, and however that gets converted to html isn't something that's accounted for.