Time Elapsing After an Offensive Penalty

[Husker John]

Texas vs. Nebraska

2:04 left in the game, a pass is complete for a first down for Texas. The receiver is called for offensive pass interference. The penalty is assessed. Texas takes a delay of game penalty. When the third down play is replayed, the clock reads 1:34 and the clock was not running at the time.

The original pass play was a five step drop and took only 6-7 seconds to run. Should the clock have been stopped following the original third down play? Or, should it have restarted following the first penalty being assessed? If so, why?