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You might try posting a chapter or two of the book, so long as it is not copyrighted, with the original HTML and the resulting epub. It might be easier for those who are very familiar with calibre to suggest how you might avoid the problems you are having using calibre's extensive preference settings. You might post the stylesheet as well, as calibre adds many styles of its own.
If you can find an actual problem with calibre, the author, Kovid, is very responsive.
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