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I had the same problem before and posted on it on this forum. Ultimately it is an indexing problem. You can tell Kindle is indexing by search for a random set of characters from the home screen. If indexing is continuing, you'll get a message that says the kindle is waiting for a file. By the way, this also eats a lot of battery, because indexing takes much more power than simply flipping a page. So if you take a lot f notes, you'll notice it.
Fixing it was rather complicated. As previous posters have noted, Kindle indexes the document/book after each note is made, but that is not the same thing as the my clippings file. You can delete that file, but the indexing still remains. A hard reset sometimes corrects the problem temporarily, but I found it to be unreliable. My solution was to delete the indexing file itself, which resides as a hidden file on your kindle. Then I let the kindle re-index everything (make sure you are connected to power). That corrected the problem and it hasn't reappeared in over two months.
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