I was having the setup issue continually. Tried factory resets a few times and reinstal of desktop software. nthing seemed to help. I did discover that if i went to home screen before shutting down or going to sleep mode that that then stopped the setup from happening. So now I always go to home page before shutting down and have not have the issue since. I also found that the issue seemed to happen more with third party books than with kobo books but was happening ocasionally with them as well. I know going to the home page before shutting down isn't a fix but it is a pretty simple work around.
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