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If it tries to create HTML tables, I don't think Kindle supports them well, or possibly not at all. If you save the table as a graphic, and embed that via an <img> tag in the html, it might help some. I know if you use Mobipocket Creator, you have to specify all the individual files separately as input, so it's kind of a pain if there are a lot of them. You might ask on the Calibre forum for more Calibre-specific questions.
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