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Some further investigation and it was the indexing issue. Or at least I think it was. I just deleted the indexing file and then let my Kindle re-index everything. The another restart. And now all works as usual. Just did dumpmessages and saw it declined less than 5% after a day of use, including wireless browsing and note-taking. So, good as new.
One thing I realized though is that the Kindle re-indexes files as you take notes. Try it...open a book/file and add a note, then immediately try to search the same document. You'll get the indexing message. Since indexing uses more power, plus the extra juice of screen updating from typing, I imagine you'll get noticeably reduced battery life if you are a heavy note-taker like me.
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