... a direct quote taken from a transcription of one of the videos Matt Cutts has been doing recently. Sure seems to me he is saying that if your site was affected, itís due to optimization. We had several sites affected, but eventually all came back; our suspicion is that they dialed back these over optimization filters.
This makes the most sense to me as a theory about what's been going on.
I think G's motivation is to combat the exploding adsense spam problem. Think about it - MFA sites are practically by definition going to be "over optimized" with anchor, title, H1, H2, H3, and body text often matching "too well".
I personally think that there has been an over-optimization dail being played within in combination with trust-rank factors.
I think that on June 27th, they turned the OO dial up hard, then backed it down on July 27th, and again on August 17th.