If the problem just started, it's probably something related to your content: Either too much, a book that didn't copy properly (and)/or a problem with the index.
Check to see that you have enough space (things start to get weird when there's less than about 200mb) and delete something if you have less than that. If that doesn't work, try deleting the documents folder contents on the Kindle (if you have a backup) and transferring the content again. It'll re-index on its own so leave the Kindle alone for awhile.
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