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Are you also using calibre to create shelves? If so, check to see if it is possible that one of the duplicate shelves is actually coming from there. There is a known issue, that Davidfor can speak to, about small differences between shelves created on the device (something about leading spaces, if I remember correctly).
FWIW, there was a beta some months back that created huge duplicate shelf problems for some people. A technician (after the issue actually went higher than Tier 2) had to manually do something to my sync stuff on the server and then I had to do a reinstall.
If this were a common issue now, I bet we'd be seeing a whole lot more complains, so maybe look at the calibre issue, if it seems possibly relevant.
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