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For what it's worth, I recommend against pre-converting and I also prefer not to have the conversion plugin I wrote be used at all. It promotes removing other formats (which I also strongly recommend against), and it makes a very broad (and incorrect) assumption that the KePub format generated is correct and will never change or be improved upon.
Can you run calibre in debug mode (see the first post), reproduce the problem, and post the debug log?
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