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I have your second problem intermittently. If I use Calibre to, for example, remove two books and add three, "My Documents" sometimes hangs at the updating box, sometimes shows the new books but doesn't delete the removed ones and sometimes gets it right. The only consistent thing I've discovered is that Calibre doesn't properly eject either the Nook or the SD card (although they disappear from the buttons at the top). I need to close Calibre without ejecting, then eject first the card then the Nook from Explorer. Upon this eject, the Nook goes from the "connected" page to my wallpaper and these are the times that at least SOME of the updates are recognized. Also, in preferences in Calibre, it seemed to help to choose automatic updating of metadata, which forces an update on each "transaction" with the Nook. BTW, these problems occur in both Windows XP and Vista. None of the problems affect the B&N Library.
Glad if any of this helps, but it's obviously not the total solution, and I'd be happy to hear from others if they have suggestions.
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