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If I recall correctly (I'm not a Kindle user), books that come from Amazon/Kindle stores will go to the books folder (or tag?) of your Kindle but anything that comes from somewhere else (like converted from Calibre) will go to your 'documents' as if it were grocery-notes or such...
Check up on that, ...
(With Calibre, in the Preferences > Output options > Mobi, there's a box with "Personnal doc tag" [pdoc] ... Erase that box and re-convert and the newer .mobi should go to books rather than documents. -- I think anyway)
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