I transferred epubs from calibre that were set up with shelves and worked fine with no duplication on my Touch, and found I had multiple shelves for only one series on the Glo, without any sync to the Kobo servers. WiFi was off. Please explain how that is a Kobo Server issue?
I'll give heavy odds it is either a Kobo internal database or firmware issue, or calibre has a bug, etc. Since it also seems to be happening to people syncing to Kobo's servers and apparently not transferring from Calibre then I'd lean toward it being a firmware bug that affects the internal database by occasionally creating a duplicate record. Perhaps, if a transfer doesn't complete properly and is restarted a second shelf record gets inserted... Who knows? Mere guesswork.