[Tim Hancock]

My guess on the penalty box is the "hold short" line at the entrance to the runway. After a pilot recieves his departure clearance, he typically calls ground control to request clearance to taxi to the active runway. Upon recieving taxi clearance the pilot is usually cleared to taxi to a specified runway. This means you can taxi to the approved runway, but you must "hold short" at a painted line near the entrance to the runway. In other words, you are cleared to the entry of the runway, but not actually onto the runway. At that point, usually you must receive additional clearance from the tower frequency to enter the actual runway. Sometimes it will be clearance for takeoff, sometimes it will be a "position and hold". After actually taking off, tower will tell you to contact "departure" who will then send you off on your intended route.