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I thought the other devices wrote a calibre.metadata file to the device to help with matching the files? Since it would be normal for the process of writing to the device to update the metadata within the file that is being sent to the device, the file inside the Calibre library is quite likely to be different to the one on the device.
As it is working via iTunes, I am not sure if the iPad driver is working in that way? If not the details for deciding the 'on-device' status may be different, and it might be necessary to force the copy of the file inside the Calibre library to have its metadata updated before sending it to the iPad.
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