I've even gone in to Alexa to start verifying all of our back-links. All of our links are from blogs / news / twitter , et al. That said, it doesn't mean Penguin didn't hurt us. Algorithms have corner cases.
It's come out that for a few thousand, you can buy black hat's who will do crappy link building for your competitors. So, possible scenario: Safe Shepard stepped on somebody's toes and they retaliated by hiring (or creating) a ton of crappy back links to the website. Unlikely, but possible.