To make the buttons work with Kindle:
1) Open a book in the Kindle app
2) Open the formatting menu where you can change text size (tap the Aa)
3) Select More
4) Select Turn Pages with Volume Controls
After you set it in once it works with other books. This also works with Google Playbooks.
If still does not work, please disable the "Scrolling Buttons" in the Navigation ball and try again.