I can't be sure that it's directly a Calibre issue, or the recent Kobo update (2.8.1) but after transferring books to my Aura HD, I now see that under Library->Selves, each Tag (i.e. Adventure, Fantasy, etc.) is duplicated 4 times, with each one containing the exact books inside. Series shelves are fine, those are not duplicated.
I've not tried everything I can think of, including factory resetting my Kobo, making sure that once it's all set up again, the Shelves list is empty. No matter what I try, it always the same now. See the pic below: