John Mueller mentioned in a Google hangout recently that Penguin is refreshing quite often. Here is the video. Start listening at about 3:52 and then pay close attention to what he says at 4:11.
He says that Penguin is rerun regularly...not quite weekly or daily. But according to what Google has announced, the only refreshes have been April 24 (original rollout), May 25 and October 5.
That brings up all sorts of questions in my mind. I'd love to hear what fathom thinks of this. I remember him saying that his testing showed that sites could be hit by Penguin on a non-announced Penguin day. Perhaps it is these silent reruns that is causing that.