It appears I have fixed the issue, but I still dont understand it. I had the back-end file parsed and setup perfectly, however, PEx would not use the inheritance untill i gave the ingame command. I normally edit the back-ends of my plugins directly, but I guess that with PEx you must use the in game commands.
Although PEx ( 1.19.1 ) is working for all the worlds and users I set permissions for, my multiverse worlds are not inheriting their parents permissions. Can someone please tell me what is wrong with this permissions.yml