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In the Windows port of libimobiledevice, I fixed a bug whereby multiple devices were reported when only one was connected. This fix is not in the Linux version, and it could be the problem here. I suggest you go into the Calibre preferences and customise the iOS reader plugin to tick the two debugging check boxes, then repeat the test - restart Calibre in debug mode etc. Post the log here again - it should be a lot bigger this time.
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