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As rebooting fixes the performance issues I assume that the reader app has a memory leak (or cache without expiration). It could also be caused by your data/books. When allocation new memory to execute simple tasks takes so long for the readet app this is usually the case.
Rebooting / Restarting the reader helps ... assigning much more memory to the process could hide the problem - anyhow Amazon would need to do this and your reader would need enough physical memory.
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