Did you manually set the time? If not, try that. It can affect the things you've mentioned, especially if the time is sometimes being temporarily "fixed" by wifi or connecting to a PC. If the time is not manually set, it will only be right some of the time. That can affect the order the kobo thinks things are being read.
Probably davidfor is right, but since not only I, but others have had the same issues when the time was set wrong, I thought I'd mention a possible easy fix.
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