I actually completely deleted the Missionscript.rul from the standard folder. Now, the mod is running like a dream.
Please never do this again. You should not do anything to edit the standard folders, as those are for the base game. Anyone who wants to use your mod would have to do the same thing. When Meridian says "delete" the mission scripts, he means to put this in your mod's mission scripts file:
missionScripts:
- delete: recon
- delete: invasion