Problem/Bug (Beta 1.7.3) Permissions not working

Recently I set up a beta 1.7.3 server with Project Poseidon (a CB1060 fork) and started installing some plugins. My permissions plugin is PermissionsEx, which I used to use all the time. Many permissions work as they should, but also quite a few don't.

All the WorldEdit permissions do NOT work. Also, a few Essentials permissions do not work. I looked at all the config files but couldn't find anything useful.

Does anyone know what this could be due to? All help is welcome!

PermissionsEx (permissions.yml):

Code:

groups:
  Player:
    default: true
    permissions:
    - essentials.spawn
    - -essentials.mail
    - essentials.list
    - essentials.motd
    - essentials.afk
    - essentials.weather
    - essentials.item
    - essentials.item-all
    - essentials.seen
    - essentials.broadcast
    - essentials.time
    - essentials.time.set
    - worldedit.*
  Contributor:
    default: false
    permissions:
    - modifyworld.*
    inheritance:
    - Player
  Staff:
    default: false
    permissions:
    - modifyworld.*
    inheritance:
    - Player
    - Friend
  Admin:
    default: false
    permissions:
    - modifyworld.*
    inheritance:
     - Player
     - Friend
     - Staff
users:
    Sperwer:
        group:
        - Player

 

Here you go:
https://pastebin.com/MxpZCXm6