Seeing as though its been a long time since i’ve done much work with Group Policies, it took me a long time to work out why the policy for disabling Windows Updates within IE and the start menu would not work, yet the settings for telling where the client should go to get its updates did work.
Eventually I read a website which tipped me off and is actually obvious when you think about it. I had created an OU and moved computers into it, but I hadn’t added the users to the OU. Therefore only the computer configs were amended but not the users.
Now that I’ve done it correctly, WUS seems to be working pretty well (apart from one machine that thinks it needs to download .net framework 1.0 patches when in actual fact it needs to download 1.1 patches.