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@jgaiser-
This may be old and not relevant anymore as I have an original Fire and don't use Calibre Companion. This problem was associated with the 'personal doc' tag of the book which can be seen in the conversion window of Calibre under 'mobi output'. If the 'personal doc tag' has PDOC as its value the book will show up as a document; if you either make the 'personal doc tag' blank or EBOK (and reconvert) then it will show up as a book.
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