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Are you trying to send to your ipad as a device?
I use calibre and my ipad together all the time via itunes. You need to go to device - connect to itunes (I find this works best with the ipad NOT connected at the same time).
Once calibre is connected to itunes and you can see the empty "On Device" column, then click send to device - main memory and it should send the book to itunes where it will be waiting for you in the books area.
All this depends on itunes being set up according to the sticky and as dwanthny said, make sure to disable the Apple plugin.
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