UPDATE: On a separate thread, Kovid posted the following:
"When you view an EPUB file using calibre's viewer it will insert that file into the EPUB. Apparently, the good folks at Apple have even less of a clue as to how to validate EPUB files, so they complain about it. If you want to use the calibre viewer to check your EPUB files before submission, I suggest doing it on a copy of the EPUB. "
So, I believe the answer is as follows: re-import the file into Calibre, run the conversion, but DO NOT view it. Just grab it and run. It worked! Thanks Kovid. Sending another donation soon.
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