Not all Custom Stories show...

[Mudbill]

Looks like everything is normal.

A CS will only show up in-game, and an FC will never show up in the game. But FCs will show up in the Modloader.

Only exceptions would be a possible hybrid (will work on both but I've never seen one) and strangely made mods that may not show up in the Modloader either (I've seen 1 case). Those would have to be started with their own .bat file.