Permissions 3 messing up? Not allowed access even with '*'

Hey I'm having a little problem (and quite a frustrating one) with permissions 3.6.1 (or 3.1.6 can't remember the order). Everythign was fine until I used my new permissions file, as i needed to update it as it had multiple nodes missing.
I am in the 'Admin' group which has the '*' wildcard in and this worked fine before, but now im denied access to CreativeGates portals, and even the permissions commands, as i wanted to check what group i was actually in. The prefixes work completely fine, but even when the command is CLEARLY in the file, it denies access. I am also unable to fly when I am in Creative Gamemode, when i could fly before i replaced the file.

Yes, I replaced the files completely without back-up... One time i don't make a back-up, it messes up...

Here is my groups.yaml:

http://pastie.org/2585179

On top of the plugins I have at the head of the file, i have these running:

BananaLogArchiver
BananaTweet
BananaMapRender
BleedingMobs
Buycraft
CustomCrafting
EssentialsSpawn
MCSL
Multiverse-Core
Multiverse-Portal
NarrowtuxLib
OnlinePlayers
phpBBmanager (or ForumAcc, but I use it outdated)
Propaganda
Questioner
Worldedit


Thanks for any help you can give me

EDIT: I am thinking of using an active permissions plugin, anyone got any strong reccomendations?