You'll need to provide a lot more information.
What version of InDesign? What platform?
It makes perfect sense to me that the page layout is not preserved and images are moved to other locations for EPUB and Kindle output. Both require much file preparation which I can't begin to describe in a simple answer. Paragraph, character and object styles must be applied. Anything in the main text flow must be anchored in it (pictures, captions, sidebars). You just make choices of how to create page breaks and how to set export order. InDesign formatting is translated into HTML and CSS which requires much preparation.
Best sources of information: (1) Anne-Marie Concepcion's videos at Lynda.com are available for InDesign CS5, CS6, and CC. (2) Elizabeth Castro's eBooks at her website:
It doesn't make sense that these things would disappear or be rearranged in a PDF file. A PDF should reproduce the page layout exactly. How did you export the PDF (print or interactive)? What PDF Preset did you use if you chose print? What PDF reader are you using? If possible, show screen captures of the InDesign layout and the PDF exported file (attach with the camera icon in the edit screen).