The cover page might still be there. An ePub opens on its first page, which is the cover image. A Kindle ebook opens after the cover page, and you need to select "cover" from the navigation menu to see the cover image.
You did not say what was wrong with the images at the end of each chapter. If they are 2x the size you expect, then add width and height attributes in pixels to the images in the ePub before conversion (see
Is there a "fix" or work-around for Kindle doubleing size of small graphics? ).