Plugin Help PermissionsEx - No permissions unless Opped

Hey guys,
I'm sure this may have been asked a few times before, however I've been trying to work on getting PermissionsEx working with my server. The problem I am having is that no groups are receiving any permissions once de-opped.

Here's the link to my permissions.yml: https://pastebin.com/Y3EpQPRL
Here's the list of plugins I use as well:
CommandSigns
CraftBook
Herochat
Multiverse-Core
Multiverse-Portals
PermissionsEx
PluginMetrics
Vault
WorldEdit

If anyone could take a look at it or offer any advice it would be more than appreciated

Thanks heaps in advance

 

I will remove the modifyworld permission as I didn't suspect for it to do anything i the first place.

Should the other permissions not work with the other group though? That's what I'm trying to figure out. Also the prefixes and so on all work fine.

 

@timtower The other groups/ranks in the permissions.yml that's in my paste bin link. Yeah I have a chat managing plugin, just reassuring that that works anyway.

 

@timtower None of the groups work when deopped, weirdly when not opped the only permission that can be used, by any rank/group, is /reload.

 

@timtower them to build and use multiverse portals. I'm okay with adding permissions, I just can't figure out why even the higher groups can't use their permissions. But yeah, thanks heaps for your assistance so far!

 

@timtower Okay it worked, that's great!

EDIT: Also quickly read somewhere that the permission '*' is what enalbes all permissions, rather than 'permissions*' I've just tested that and it seems to have worked - with the Owner group this is

EDIT2: @timtower I've added some bukkit permissions (bukkit.command.me and so on) and they are having no effect.