What happens when you turn all iterations of cover display off? That would mean changing the options in settings and perhaps also in how your "books" list appears.
What Kobo reader do you have--WiFi or original? What version of the firmware? Which desktop application do you use, and what version of that are you using?
The two versions of the reader don't seem to do resets the same way, in terms of what one has to do to get a truly clean install.
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