One of the main reasons for the radical improvement is due to the fact that cool air is being vented directly onto the CPU. Under normal conditions with a stock cooler the already warmed air in the box is being blown over the CPU. The flow patterns of a box are very critical for good air cooling. Most boxes are very bad at managing air flow. Anandtech did a very good article about three years ago that showed just how important box design from a air flow point of view is for cooling.