I had this problem initially with your excellent D7000 book where the pages were out of skew and there were large spaces between headings etc. E.g. The new header would appear at the base of a page, then the subject text would start on the next page. This is happening on the D800 book. Then, mysteriously it sorted it's self out but after a ipad update. I am using iPad3.
It's not a show stopper, but spoils the visual effect and I am looking forward to reading it. Of course it could be a problem with my iPad Kindle App Perhaps the layout's meant to be like that of course.