Make sure the name of the mission folder and the names of the files inside the folder match exactly.
Also name the folder and files inside in the same manner as the other folder and files. Such as SM01 Battle of Midway or SM Manila Patrol
Here is a link to a manual for the mission editor. It's for sh3 but sh4 is much the same. (thanks to peabody for the link)
http://nordfront.org/xvii-downloads/...editor_v12.pdf