Well, /halt only stop the processing of that event, when mIRC is looking for an event to trigger, it checks your script file in order and triggers one event (if applicable) per file.
@Gargantuan: You have no other choice than to make both script aware of the others and/or work together. If they are events based, you can use the '&' event prefix or check $halted to check if a previous event was already halted
