running, keeps the clock running after the penatly is enforced, but the play clock is reset.  This is an excellent way to get an extra "down" of clock to run off.  Maybe it's different in the last 2 minutes but BYU's false start penalty late in the 4Q on 2nd & Goal with 4:30 on the clock (and .01 on the play clock) led to an extra 20 second run off before we ended up hiking it on 2nd down.