The file and folder names are not the same as the Mission name.
This is what you see in the Single Mission menu (Quick Mission in Stock & some other mods), the files are in SingleMissions folder
---------------------------
This is what you see choosing the War Patrol. Those files as you know are in the SinglePatrols folder
------------------------------------
In both cases, the naming convention is for ease of author cataloging. Don't look at the folder name and file name as the mission name:
You'll find the Patrol files done the same way. Ubisoft had their "nomenclature" of a leading SM for single mission folders and WP for War Patrol folder names. They would then number it and give it a name the same as the mission name. You can name the mission whatever you want, and name the file and folder something totally unrelated...
Now, if the files aren't in the folders, or your menu doesn't look similar to above, then there's a problem.