One of my best sites that ranks really well and gets good traffic from Google (and was not pandalized), had its TBPR stripped from 3 to 0 in mid-February. Since it doesn't sell links, but did have 4 follow'd links that perhaps Google thought were paid, I nofollow'd them, put in a reconsideration request, and waited.
Today, approximately 3 months later, the TBPR is back to 3. Last time I checked was a few days ago, so the change is relatively new. Not sure if the change is due to an update that might be happening for everyone, or if it's specific to my site only, after a 3 month penalty was lifted.
In any case, thought I'd share, in case anyone cared.