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Have had the same problem...it's a iTunes thing. The solution I've found is to start up iTunes and plug in my iTouch/iPad before I start Calibre. Then when you start up Calibre (at least with the newer versions) you get an alert suggesting that you disable the Calibre device driver. Do so and then choose Connect/Share 'connect to iTunes'. Now you should see the 'send to device' icon. When you send a book to Device, or drag a book into iTunes, it goes into the 'Books' folder in your computer iTunes library. I just open that folder and drag the books into the 'Books' folder on my iTouch/iPad. You should see the book syncing and when you eject and open iBooks on your iPad, the books should be there.
As I mentioned in my previous post, I like the combination of the dropbox and Stanza better for my iTouch, but my friend uses iBooks on her iPad which is why I'm familiar with this problem.
cheers
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