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Note that if you are using the Connect to iTunes method it is not necessary to have the iPad plugged in at the time you send books to iTunes from Calibre. You can later sync iTunes to your device at a convenient time regardless of whether Calibre is running.
The other point is that it is a good idea to have the Apple Device driver under Preferences->Plugins->Device Interface plugins disabled. This stops calibre from directly detecting an iPad/iPhone/iPod directly if it is plugged in so that all the interactions continue to go via iTunes.
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