The clock will start based on the reason that the clock was stopped. For instance, if a first down running play gains 5 yards and during the play there was a penalty the clock was stopped for an official's time out to administer the penalty. Since the official stopped the clock the official (referee) will start the clock. Conversely, if the same first down play was an incomplete pass and a penalty occured, the clock is stopped because of the incomplete pass not for the penalty. Yes, we will adminsiter the penalty during the dead ball period, but the clock was stopped for the incomplete pass and will start on the snap.
Hope that "clears" it up a little!
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Dave
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