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You may have discovered one of the reasons why PDFs are poor source files for ebooks - the conversion processes can't figure out what to do with the images in PDFs. The Calibre site states ....
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The PDF conversion tries to extract the text and images from the PDF file and convert them to an HTML based ebook. Some PDF files have images in a format that cannot be extracted (vector images). All tables are also represented as vector diagrams, thus they cannot be extracted.
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