Updates and tuning for Panda and Penguin are rolling out periodically: searchengineland.com/library/google/google-penguin-update And especially: searchengineland.com/library/google/google-panda-update/panda-update-news
When 90 percent of your keywords get shuffled, you would definitely think of something has happened at the top level.
Ninety percent? Where is your evidence of this? Ninety percent of keywords you track? Which might only be 0.0001% of keywords in existence. As you can see here: http://www.seomoz.org/google-algorithm-change At the time of the OP's post, the Panda update hadn't happened yet, but there had been a new round of links discounted (which would affect rank) and emails sent out.