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.
http://www.opensiteexplorer.org/domains?site=safeshepherd.co...
http://www.branded3.com/seo/penguin-update-renders-seomoz-ma...