Doing a search for ;dm from the home screen on your kindle will dump the device's log files to your documents directory.
One thing to try would be to sideload a book that isn't working, disconnect USB, give it 10 seconds or so to try to find the book, use the ;dm command to dump the logs, and copy them to a PC/Mac for examination. Perhaps there will be an error message near the end of one of the log files that might point you in the right direction.
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