PermissionsEx Problem

I've recently come back into minecraft and with that comes the desire to set-up another server. On my previous server I used GroupManager which I rarely had any problems with but apparently now it's discontinued and highly not recommended so I went back to searching and it wasn't a surprise that I stumbled across PermissionsEx- which seems to be the most popular permission plugin available right now. I can't seem to get PermissionsEx to listen to me and it's becoming pretty frustrating.

Here is the just of it. It just doesn't seem to be working. No errors but no permissions. After messing around with it I finally managed to get Prefixes to work but I had to use the commands because it wasn't listen to my code, then I attempted to essentials.kick to "mod" which failed, so I used a command, which also failed, then I noticed every-time I reloaded I was placed back to the default rank.

Plugins I have Installed:
EssentialsX
EssentialsXChat
PermissionsEx
Vault

I've been tinkering around with it for some time now and I can't seem to find the solution.

Here is my PermissionsEx > permissions.yml

Code:

groups:
  player:
    options:
      default: true
      prefix: '[Member] '
    permissions:
  mod:
    options:
      default: false
      prefix: '[Mod] '
    permissions:
    - essentials.help
    - essentials.kick
  admin:
    options:
      default: false
      prefix: '[Admin] '
    permissions:
schema-version: 1

 

@HatLicense

Try change:
permissions: to permissions: []

And you don't need to set the default to false for every group.