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I've had the same exact problems with two different Kobos and the problem was solved by using calibre to create the collections and load all ebooks. Unfortunately the latest version of calibre, 2.12, doesn't work with the latest firmware upgrade from Kobo, 3.12. But I understand that a new version of calibre is forthcoming in the next week or so and hopefully that will solve your problems. It worked for me previously. See the sticky topic -Quick Guide to Shelf Management and it will walk you through how to set everything up.
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