Yes, it is probably due to the time problem you have had. My KT hasn't had this problem yet, but I saw it occasionally with my K3. It seems that the internal clock would get out of synch with the real world some times. If I reset the clock to the current time it would 'fix' itself.
I don't know how all of your hacks interact with this problem. However, assuming its just the time and that you have a book 'stuck' at the top, then I would first rest/change the time. Then I would delete and re-add the stuck book. Now try opening up a new book and see if it goes to the top.
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