Hierarchy of actionscript?

What gives? I’m using MovieClip.prototype code in my movie. I put it in the first frame of the main timeline with a stop();. The code affects the MCs like it should. When the timeline plays to the next keyframe with a stop(); in it the MovieClip.prototype code doesn’t affect the MCs at all.

Why does a simple stop(); kill the MovieClip.prototype code? :puzzled: