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If the books from other stores were already flagged as personal documents, calibre won't change that metadata (though I admit to being puzzled as to why any "other store's" mobi's would be flagged as personal documents). Perhaps you sent one of these books to your kindle's email address for conversion? That would definitely mark them as pdocs.
The only magic I know of to alter that metadata is mobi2mobi from the MobiPerl tools.
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