PermissionsEx Not Working!!!

Hey,
I am currently in the middle of setting up a server for the public to play on. However, my PermissionsEx plugin is not working. When I type in pex user TPCBonehound group set God in the console, nothing at all happens. When someone new joins they have none of the permissions that I have set for the 'Initiate' group. Here is my permissions.yml: http://pastebin.com/T0pGuShH

My config.yml looks like this: http://pastebin.com/npUuBVrE

As for plugins, I have:
Factions, NoSwear, AutoBroadcaster, AdBolt, AntiBuildPlus, AutoRank, Buycraft, ChestCommands, ChestMaster, Citizens, ClearLag, CustomEnchantments, CustomJoinItems, Denizen, NoFall, EAuctions, KingKits, KingKitsSpecial, MassiveCore, Multiverse-Core, Multiverse-Inventories, Multiverse-Portals, PEX, Essentials, NoRain, PerWorldPlugins, SpawnTP, WorldChat, WorldEdit, WorldGuard

If someone could help me out that would be great, thanks!