Ok chaps, I realise there have been a series of miscommunications and problems about the Minecraft server and why permissions haven't been working.

Firstly, a little history of the addons used which have broken, and are causing these problems.
The minecraft server runs with ‘Craftbukkit’, which is a base addon which the other addons we use are based within (in simple)
The two current addons which have updated without waiting for craftbukkit are iChat and Groupmanager.
iChat is easily fixed, and has been, however GroupManager is not, and has not.
What has happened with Groupmanager is that it has wiped the userdata file, which stores everything about the players on the server, including Ops, Mods, donators, ATK members and guests, and deleting this file has meant a lot of the information has been lost.
Some of the data is twinned in other files, so those elements (such as homes) haven’t failed completely.
The core of our groups ([ATK] [Op] [Mod]) is in that userdata file, so when it was wiped, we’ve lost all of the groups.
This wipe coincided with Katakuna (bxnub) and I leaving to go to LeachLAN 7, which, being a small LAN, blocks many ports to games so we were unable to repair GroupManager while there.
When I got home last night, I briefly messed around with the manager tools and found that being Server Op doesn’t correlate with Op group when it comes to addition rules, so basically I cannot do anything client-side, and I don’t personally have access to edit the userdata file to give myself access clientside.
Any questions may be asked, I hope I’ve made it clear that until Katakuna is around nothing can be done with the ATK Permissions.