I am having a similar problem with an EPUB file that I converted to MOBI. I set up chapters, and it works great, except for one. It should say :
as one chapter. But, for some reason, it puts "Part One" on one page, and "Prologue" on another page. I've checked the code, and there is no difference from all the other chapter headings. In the EPUB file, it works perfectly. In the Calibre viewer, it's perfect. But, on my Kindle, and Kindle for PC, it's not.
I even merged this with the next chapter, and it still does it. I've spent 2 days trying to figure this out. I've posted to other forums, but have gotten no responses.