Sideloaded Duplicate Shelves on the Glo, and a simple solution...
While I realize others have experienced duplicate shelves on their readers and have expressed belief that it is a Kobo server issue, I have encountered the problem with side loaded epubs via Calibre which is being used to create shelves. I do not have any Kobo books on my reader, all my books are without DRM, and yet on one series of three I experienced multiple shelves after transferring the epubs to my Glo.
I noted the duplicate shelf, reconnected to Calibre, deleted the titles, sent them again, and then found myself with two duplicate shelves for the same series! I tried again and got the second duplicate to go away, but had no luck with rinse and repeat as far as the first duplicate was concerned.
My ultimate solution, while far from inspired, was to delete the epubs from the reader, change the contents of the metadata series field for the three titles in Calibre, send them to the reader one last time and watch my problem disappear. I cheated, by merely changing the series information to a slightly different shelf name.
Far from an awe inspiring feat of legerdemain, but it worked.
I suspect that there may be a Kobo firmware issue or database issue that may be contributing to this whole duplicate shelves issue, and am not quite sure it is really a Kobo server side issue. I think it far more likely that it is a firmware issue, since multiple shelves can apparently be created without so much as a sync to the Kobo servers of any kind.