The flavor sample between primary and secondary differ from that of the final brew. It's really just an indicator of whether your beer is on track (not infected, or other gross problems). After the yeast do the post-ferment clean-up, you carbonate, cool, and age (for the time it takes to do all this), the flavor profile will be strikingly different. To my palate, "grainy" flavors are especially quick to fade during this period, and I'm guessing your "chocolate" is in that category. Which begs the question: what the hell is wrong with chocolate???