I've revised the FAQ in
Calibre + iPad: Start here to recommend restarting calibre after disabling the device driver. I found that disabling the driver and then Connecting to iTunes in the same session could cause the problem.
Using the 'Connect to iTunes' approach is simpler than using the device driver, requiring far less fiddling with iTunes settings. Mixing the two approaches can lead to unpredictable and unintended results.
G