Something is adding brackets automatically? (Permissions)

I have PEX on my server and when I set the brackets around a group, it has two of them like so:

[[ Admin]]

This is really ugly and I want to fix it. I run 2 different servers. One off servercraft.co and one out of home. The one I run at home doesn't automatically put the brackets in. Let me show you the files of the servercraft.co (it's a start up server)

Essentials
EssentialsChat
EssentialsProtect
EssentialsSpawn
PermissionsEX
WorldEdit

That is all.
You can see my permissions file in the pastebin link below:
http://pastebin.com/9BMvKGYz

So as you can see, I've tried to remove the [ ] brackets around the prefixes, but this occurs

[Admin]InvaderIan

No space in between the prefix. Me and another admin have been playing around that for a few hours, tinkering with the prefix white spaces and Essentials config (the EssentialsChat part).
We also found out that McMyAdmin, a program included with the servercraft.co hosting company, has it's own permissions thing. Is that's what causing it?

If you really need it, my EssentialsChat part of the config is here:
http://pastebin.com/r83gecJE

As you can see we didn't edit that part. When we did it just broke the displayname and prefix more.
Thank you SO much for your time and I hope you help me! Have a nice day :>

- Ian