I received this message for one of my sites in my webmaster tools in the middle of December. When I noticed the message I checked all my rankings and there was no negative fluctuations, if anything the majority of my rankings went up. Until Jan 8th, when a good chunk of my higher traffic keywords, including the root domain rankings all dropped between 5-10 positions, NOT pages!
Some of my rankings stayed put at #1 on a few pages, and my PR still remains intact.
I'm not sure if this is a penalty, or just a site wide dance. If it were a penalty I feel as though it would be a lot worse and ALL my rankings would be affected from what I;ve read so far from other people.
If you have experienced this message before I and I'm sure others would appreciate if you could answer some of these questions.
When you received the message did your site drop in rank before, same day, or after?
How far did your site drop and was it across the board with all your keywords or just a few pages and root domain?
Did the site ever come back and how long did it take?
If yes to above, What did you do to get it to come back? I heard the penalty lasts 90 days if you do nothing and then will come back by default.