I think there is somekind of default timeout or interrupt or something..I haven't coded in any thing but 1.3. But I noticed that when in the normal game and you run a script on a another race, once the scripts is done, or sometimes before that it will break and start a default action.
Also the interrupt signals can mess with them too..as with the new attack AI if you don't have all the new scirpts inited, and you run the new combat script on a ship, it will revert back to the default scripts when you attack because the default interrupt script will call and that script calls the default combat script...thats what I know.
"Try not. Do or do not, there is no try."-Yoda
"[Its] time for the human race to enter the solar system"-Dan Quayle