I've been having the same problem, it's only been happening in some of the books I've read in the past week or so. I'm a newbie when it comes to Kobo and since it started happening after I connected it to my notebook for the first time I assumed I messed up something in the settings (before I only had connected it to my desktop). I was planning on doing a factory reset when I finished my current book to see if that would fix it.
Sorry I can't be of more help.
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