ND-OU game, OPI was called in the EZ with :15 or so left in the game. OPI allowed the receiver to catch the ball for a TD which stopped the clock. No zap was used. Is that not a penalty that caused teh clock to stop?
You're not grasping the concept. With a live-ball, you need a foul with the ball that causes the ball to become dead and the clock to stop. In this situation, the clock was stopped due to the apparent touchdown. In the heirarchy of what stops the clock, a score trumps everything, followed by touchbacks, then out of bounds, then incomplete passes, then awarding a first down, and, finally, to complete a penalty at the bottom of the heap. Even if he had not scored, the clock would have stopped either to complete the penalty or to award a first down. In none of those situations was there a FOUL that actually caused the clock to stop. Check the rule and the various CFO bulletins. The live-ball fouls that cause the clock to stop (before a change of team possession) are illegal incomplete forward passes, an illegal backward pass out of bounds (to conserve time), and an illegal kick by Team A. Someone else may know of something else, but those are all the live-ball fouls I know that cause the ball to become dead and the clock to stop. There are no live-ball player-on-player or "procedural" fouls that cause the ball to become dead and the clock to stop. Something else will cause the clock to stop. But, even if there is nothing else that stops the clock, stopping the clock to complete a penalty does not qualify a penalty for the 10-second subtraction. The foul itself has to immediately cause the clock to stop (as in the case of intentional grounding, at the moment the ball hits the ground).
If the ball is dead, any foul committed while the clock is running will qualify.
Another thing that may help you remember the concept is that this rule is intended to prevent a team from gaining a clock advantage by committing a foul. In the case of PI, holding, BBW, IBB - the offender has no way to know for certain that the foul will be called, thus resulting in a stoppage of the clock to complete the penalty. With ING, the passer knows that an incomplete pass will stop the clock, even if ING is called. He still gets the advantage of getting the clock stopped. This rule tries to mitigate that advantage.
