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I suspect that the azw3 format file hasn't been updated. You can check by doing Edit Metadata on the book and double clicking the azw3 file.
FanFicFare creates and updates epub format by default. Kindle generally requires mobi or azw3 Amazon specific formats. Depending on how you send the book to Kindle, the conversion may have happened automatically the first time (Reading List for example).
FFF has a setting (lower left corner of 'Basic' config tab) for 'Automatically Convert new/update books'. If you use Kindle (like I do), you probably want that checked.
And make sure that Calibre is set to Convert to azw3 by default (Preferences > Behavior > Preferred output format).
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