I have had this very same problem. Just for giggles, I decided to try making the epub using Sigil. And it worked!
I noticed a difference on the top of the page of each file. In the Sigil creations there was this:
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
"http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
In the Calibre creations there was this:
<?xml version='1.0' encoding='utf-8'?>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
I don't know what any of those heading do, but I do know that the Sigil version did get accepted by Amazon. And the Calibre one did not.
I don't know where else to look for differences but I didn't find any. There may be other places within the book, but not that I was able to find.
So, either use Sigil for now, or change the headings in your books to the Sigil wording. It worked for me.
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