Stopping or pausing code from playing

just one problem i havent been able to figure out for a couple of days, is there a way to stop or pause code from playing?
at the moment i have:

  1. my home page which has shapes mving around randomly in the background
  2. when the user click on one of the other pages it loads in the swf (movie) into a container
  3. when the user clicks the home page it unloads the movie.

however it seems to be slowing down having the moving objects as they are obviously still moving when the movie is on top of it?
so i was wondering if i could stop the code from playing, i tried using stop(); but either i am using it in the wrong way or its not what im after.

thanks