Have you recently updated Warcraft version?
Anyway, the famous issue is the map name (in the Maps Folder) has more than 44 characters (afair), it counts folder which the maps located at.
Ex :
Maps/My Map/Special Maps/The Elite Warfare/The Elite Warfare Chapter 1 Part 1 - Against All Odds.w3x
Won't appear, since in total it will over the limitation (includes all subfolder toward the map file), but :
Maps/My Map/Elite Warfare 1-1.w3x
Will appear.
That's how it works afair.