because running uses a completely different set of biomechanics. every time he ran during the game, he ran, primarily, in a sagital plane. very little faking or extra fancy stuff for more yards. the lcl pulls on the lateral side of the knee, attaching to the fibular head. the orientation of the fibers allow for a walking/running motion without much stress.
however, when it's your planting foot and you use a lot of torque to throw the football, it pulls on the lcl more, which reaggravates it. it's taut in knee extension and relaxed in knee flexion. however, it is under a lot more tension upon tib-fib rotation or femoral rotation while the foot is planted. on an already sprained ligament, it causes more pain and damage.
to all humans, there's a psychological component to injuries... after having one, your body will compensate to avoid any movement or action that might reaggravate the injury. this is my theory why he threw so poorly against the cowboys. he was at a biomechanical disadvantage with his injury so he couldn't throw the way he normally would have. an injury in the knee can cause a kinematic chain of myofascial differences from normal, which could ultimately affect how much power is put behind a throw or the angle and angular momentum at which the ball is released.
it won't be until the knee is fully healed and the knee brace is removed that he'll be back at tip top form.
here's a video where you can see that you can go from having a relatively stable knee as it moves in a saggital plane and then see the affect after the knee is under stress simply by being the planting leg for a quarterback...
http://www.youtube.com/watch?v=91kWLFxvFcg
watch from 1:25 to 2:40. you'll see everything i just explained played out and why it was an issue against the cowboys, which was probably part of why they ran the ball so much that game.