I ran into this problem myself when making my aircraft holding pattern script (see signature).
My conclusion was that player-issued commands take precidence over scripting commands. If the AI is currently on a "halt" or "move" order issued by the player, they will ignore all scripting commands, until they complete their move, or are told to "fall back into formation". I couldn't find a way to get around this, but if it is possible, I'd love to know.