Is it a version 3 map? (You can check by opening it in notepad)
If it isn't, the game protects you from crashing by ignoring map files that are out of date.
Edit (for attention):
If your map is in the manifest file, you've put it in the right location, and it's still not showing up in the appropriate spot (Small,Medium,Large), open it in notepad and confirm that the version is 3. Version 2 maps will not show up no matter what you do, because they will cause a crash if you try to load them.
If you've got a version 3 map that won't show up, and you've edited your manifest file properly (don't forget to change the count at the top!), email support with the two files.