[Katsunami]

First off, you could probably circumvent the problem by using the option mentioned above: just have calibre remove the first image/page from the book, assuming that this could be an unidentified cover page. Then Calibre will insert its own. This way, you'll end up with one cover image, regardless if the EPUB file has correctly identified it, or not.

I've chosen to fix the file itself, because when using the above option, I'd be relying on Calibre to fix a broken EPUB file, and I don't like to do this. I want my epubs to be as perfect as possible, to try and insure future convertablility if needed. (Yeah, you could call that an OCD if you really wanted to.)

After making both books exactly the same with regard to file naming, I've made sure that both of them where the same, changing Deception Point to match The Sword of Shannara. There were two differences:

TSOS used the div-tag around an img-tag to display the cover, where DP uses a p-tag.

Changing this did not resolve the problem.

And, TSOS had this in it's OPF file:

  <guide>
    <reference href="Text/cover.xhtml" title="Cover" type="cover" />
  </guide>

It was just below the <spine>-section, at the very end of the file, just before the closing </package>-tag. I've put this into the OPF file of Deception Point, at the same place, and converted to AZW3 again. Now Deception Point does not show a second cover when opened as AZW3 in Calibre.

It seems that this set of tags explicitly makes cover.xhtml the cover page of the book. I suspect that, when you omit these tags, that Calibre assumes that the book does not have a cover page, and then inserts its own.

I'm going to test with a few more books (3, to be precise) which also have this problem, and see if it resolves it.

======FIX======

edit: It seems this is it. I've tested it on three books. To make sure that everything worked as intended (and I could blindly copy-paste the part of the code above), I did the following in Sigil:

- Change the cover page name to "cover.xhtml".
- Make sure the title tag in the cover page reads:

<title>Cover</title>

- Rename the cover image to "cover.jpg". (Make sure it actually is a jpg, of course. Otherwise, use the extension the image already has.)
- Right-click the cover image, and select "Add Semantics -> Cover Image".
- Add this code, just before the </package>-tag in the OPF-file:

  <guide>
    <reference href="Text/cover.xhtml" title="Cover" type="cover" />
  </guide>

- Save the EPUB.

(The above will of course work with different filenames too, if you adjust the <reference>-tags. I do not know if it is necessary to set the <title>-tag of the cover page to the same name as the "title"-property of the <reference>-tag; I have not tested this.)

You can do all of this in the EPUB that is already in the Calibre library. Just open it directly from the Calibre library folder using Sigil. After doing this, remove the other formats such as AZW3, and recovert. I'd store the new EPUB in a different place, outside the Calibre library. Alternatively you can also do this on a backup copy, remove the book from Calibre, re-import, and then recovert.

The Calibre AZW3 format now only shows ONE cover in the viewer, as does the Kindle.

Note:
1. This is probably not a specific Kindle problem. It may happen when you convert to other formats than AZW3.
2. The Kindle starts the book on the first page after the cover cover page. As far as I know, if you want the Kindle to show a cover when opening a book, you must make two cover pages; deliberately.