I wrote two stories in Scrivener and created (compiled) a Kindle doc for each and an ePub doc for each, Rather than showing the cover image as the icon for either story in Kindle for Mac or my ePub reader these applications show a default cover instead. Opening the story in either application shows the cover (for either story) as page one.
BTW, in pdf docs created in the same way show the cover as the icon for the pdf. I hope this makes sense. I used a "Front Matter" folder for each cover image.
I'm new to Scrivener and compiling my first book to pdf (manuscript times new roman). I had similar concerns re: book cover. I added Cover to Manuscript as untitled. After compile book cover appeared as third page in left column. I drug it up above title page. I created a pdf with the cover as first page of document. Hope that helps you.
My problem: A few chapters in pdf show Chapter Titles but no body to the chapters. Yet when I go back and look at the manuscript the text for those chapters is there. I must have hidden the text somehow. Well it's late. More on this tomorrow. Cindy
Your issue may be with the Kindle (or Kindle application) and not with Scrivener. Amazon has its book display system set up so that the first page of the text--not even front matter--is what you get when you open the book. If you swipe left instead of swiping right, you will see your cover. Several epub display programs exhibit the same behavior. Has nothing to do with Scrivener.