Turn off the automatic start of the storyline while making it, god damn it!
Didn't he just explain in the post above yours that autorun has got nothing to do with the problem? Autorun starts the STORYLINE after clicking on DYOM. He is talking about MISSIONS starting after each other without even getting to the mission trigger. Autorun, whether on or off, has got absolutely nothing to do with the missions starting after each other. It only enables the storyline to start automatically.
You can try to start the compiling the missions again in a new DSL. Maybe that might work.