title_body: Pages do not always break in the same place, why?
upvoted_answer: I have experienced these kinds of problems several times on both e-ink devices and kindle apps on mobile devices. It has to do with the device's screen rendering and is probably separate from note-taking.  
  
  This is a normal kind of "confusion" for reading kindle devices. I usually encounter these kinds of scrambled pages issue when first reading an ebook. But as  I go through the book, the kind of scrambling usually  disappears. 
  
  It may have to do with memory limits or just that kindle is slow in rendering things properly. Sometimes complex formatting or unsupported CSS can cause this problem. But as I said, this thing usually disappears after you page back and forth once or twice. 
  
  The epub standard specifically allows reflowable ebooks -- so it is not guaranteed that the end of the page will be the same. If you change font size for example, the position of the page end will have to change. This is normal. 
  
  By the way, as an ebook publisher I can hard-code page breaks in the style sheets so that they are consistently on the same page. Also, fixed format ebooks will keep the same pagination (but there are disadvantages to doing this). Unless this happens for only one book or on several devices for the same book, I would not be worried about this.