I don't own a 360, so take my question with some caveat: Do you use your Pocketbook in library mode or in folder mode? Folder mode should be better to handle large collections.
And are you often adding and deleting books? Than it may be that there are some "rests" in the internal database and you could try cleaning the library (don't know if this function exists on your reader and how it is named). But this will delete all book links like last page read and so on too.
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