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Yeah... I can confirm there is some really weird behavior there with Calibre Companion if you launch your books that way. May want to avoid the update if that's how you use both of those apps like that. I just use CC to get the books on my device via the wireless connection. Then I import with Mantano into the db (it leaves the epub in the folder it found it) and launch from within Mantano's Bookshelf interface. So this doesn't really affect me. Hopefully that gets fixed for others, though.
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