I had kinda related (i think.. that is AI behaviour with invidual or wing order were different) issue when i got ships with invidual orders to operate in different ways in different waves.. That is in first wave all enemies attacked. In all subsequent waves only one ship per wing attacked and others were just hanging around the shooter so that if the shooter was killed the next ship started firing and so on. When i switched from invidual orders (removed them all) to wing orders all the ships in the wing in all the waves attacked as they should have done all the time.