End of Half Delay of Game Question

[theboys]

I was watching a GA high school game Friday night, and saw an unusual end-of-half situation. I'm not an official, so don't know all the rules, so am looking for an explanation.

Team A had the ball on their own 10, 4th down, with the clock winding down. Team B had used their timeouts, but knew there was enough time left in the half that Team A would either have to punt or take a delay of game penalty. Team A decided to take the penalty. The ref stopped the clock while the penalty was marked off, then started it again once the ball was set. Time ran out to end the half. Team A ran to their locker room, while Team B's head coach engaged the ref in an animated conversation.

My question is, does the clock start after all offensive penalties are imposed?