Copy not flowing correctly in epub format

Fixed-layout EPUB is a difficult and problematic format. In short, it either works or it doesn't; if if doesn't, there is not much you can do to fix it.

EPUB is also highly dependent on the reader used, and hardly any two render pages the same way. Even for a fixed layout, expecting the pages to exactly match the print layout is not realistic. (If you want perfect digital page images, use PDF... that's what it's for.)

EPUB requires meticulous attention to detail in the layout and styling of the InDesign document, including use of defined styles for everything, all elements anchored in a single text flow and absolutely no spot overrrides of things like font, color, spacing etc. Many things you can get away with for print or PDF (but shouldn't do anyway) will break on export to an electronic format like EPUB.

Since your book appears to be all text, I'd suggest you work to a reflowable layout instead. It's the proper format for modern e-books. Fixed-page export can seem like the simple and obvious choice, a parallel to PDF, but it's not: it's really something of a mess both technically and for readers to handle, and should only be used for "picture page" books like children's books and graphic novels. Books that are all or largely text are far better served by the 'liquid' reflowable format.

Here's a basic overview of EPUB requirements and issues: http://www.nitrosyncretic.com/DPR/dpr_indesign_epub_basics.php. There are some other essay/tutorials there as well.

Happy to answer questions.