If you had various books hanging around, and one or more of those books had something wrong with it (not entirely uncommon with books obtained in non-standard ways), the presence of that "bad" book can screw with everything else.
I would try removing everything from the SD card and doing a factory reset. Then add in the books in such a way that you can tell what book is screwing things up. Some folks do this by adding them one by one, others by doing them in batches and then narrowing that down to smaller groupings once they figure out which batch it is in. It's quite the job if you happen to be one of those folks who have thousands of books to sideload.
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