BJ has always (as long as I can remember at least) used his guard as a defensive tool. If he ends up in full or half guard, he whips in a butterfly hook and uses it to stand. I think he used his guard to put Matt Hughes in some trouble towards the end of a round in their 2nd fight, but other than that I can't remember much offensive guard work from him over the years.
Also, BJ was up against the cage the entire 3rd round. It's really hard to move and create the angles you need to be effective when you are stuck against the cage like that, especially when Jon Fitch is essentially throwing a 3 minute long combination at you. Propers to Fitch for never letting up the pace and giving Penn a chance to get the fight back to a standing or clinched position.