[I'm goin' down]

Try this.
1. Drag a mission file folder that is not working and that is in the single mission folder to the desk top.
2. Open the dragged file folder. If the mission file (mis.) is a file that you see when you click on the dragged folder, the foldler/file are in order, and restore the dragged folder back to the single mission folder. Make sure the dragged folder has the same name as the mission file.
3. If however, you see another folder (I will refer to it as the "subfolder.") which you are required to open before you see the mis. file, that could be the problem. In this case, drag the subfolder and its contents to the single mission folder and delete the empty master folder that is still on your desk top. Make sure the name of the subfolder matches the name of mission.

That might solve the problem, and if it does, you owe my crew 10 gallons of ice cream.