The short answer is just that you haven't cooked it long enough. This recipe calls for your piece of beef to be diced before braising and that cuts down on the cooking time considerably. At the two-hour mark, test a piece. If it's not tender enough yet, let it continue to cook, checking every 20 minutes. Don't give in to the impulse to turn up the heat, you're just going to dry out the sauce. If it's starting to look dry, add a little more beer and bouillon.