Well, I'd sync'd a few times checking for the 2.8.1 update and everything's been fine with no shelf problems and I got the new update a few days ago. Then today I figured I'd sync to clear out the download cue for the books I bought during the last code contest. Everything downloaded fine, but when I went to put the new books on my TBR shelf both the Nonfiction TBR and Read shelves were showing up twice and the old 'test' shelf re-appeared again. I can't delete or rename the "new" duplicate shelves. Going through the proper actions works, but the shelves stay put and their names don't change either. The test shelf deleted again just fine.
The other thing odd that happened is that the book I was currently reading stopped working. I was at the start of chapter six, but when I tapped the book to start reading where I'd left off the header & footer would show, but the rest of the screen stayed blank and the device was completely unresponsive. Putting the device to sleep brought up a blank screen (no cover or Sleeping text) and I'd have to activate the wake switch twice to get the device to do anything where it would then act as if it was re-starting (little square loading boxes). So I re-loaded the book (Calibre kePub) and it seems to be working fine. Of course a subsequent sync went just fine.
Posting it here in case any of this sounds familiar to anyone. Haven't contacted Kobo support as of yet.