This was with the new Glo as I wrote above. When I set up the reader the only thing it did was update the firmware and download/attempt to download some epubs from Kobo. I'm 99% sure no shelves appeared post sync -I recall checking, but I could be remembering incorrectly as I wasn't exactly in dispassionate observer mode, more like big kid with a new toy mode.
However, if the shelves were created then I'm pretty sure I would have noticed duplicates.
I was out, having just bought the ereader, and having some cheddar mushroom soup so thick the spoon would almost stand up and a steak sandwich in a bar/restaurant that had WiFi so I could update the firmware and log in. I transferred a few books via Calibre from my X41 tablet/convertible and read a bit while eating.
Later that evening, I sideloaded the rest of my library via Calibre, everything went fine for all but one shelf/series which created a dupe when I checked after disconnecting the Glo from Usb. I did not do a Kobo sync either wirelessly or through a pc, WiFi was off.
I had one duplicate shelf, erased the three books on the shelf via Calibre, and it went away. I reconnected and sent via Calibre again and had the shelf back and two duplicates. I did the delete again and was left with the original shelf and one duplicate. I gave up for a few days, then deleted the three titles, renamed the series in the metadata and transferred the books back to the Glo and now I have 10 shelves with varying numbers of titles and no duplicates on the Glo exactly as I had on the touch..
Subsequently, I've synced wirelessly and experienced no more duplicates... so if it's a server issue, why the 9 shelves with no problems and no more problems with the renamed shelf? Or is the issue only when the shelves are created? Then why no dupes when they first appeared? I'm clueless.