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Whilst not a "smoking gun" I wonder if some of the problem might be down to battery calibration? If the device has been factory reset at varying battery levels then charged or allowed to run until it switches off, then the battery management might be messed up.
You get problems like this on phones when you flash custom firmware, and normally you charge to 100% then wipe the battery stats and plug it back in and let it charge once more. I know it doesn't explain the problem with side-loaded books, but it might be something to consider.
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