Does your mod target both story and GM mode? A couple people reported that didn't work. And indeed, I'm not able to get my skills to show up in GM mode with targeting Story and GM mode. This is definitely a very inconvenient bug, meaning we have to maintain two different versions of a mod for story and GM mode =/ I'm going to check just targeting GM mode now.
Skills have a "ForGameMaster" check in the stats. That should be all that's necessary.