I have set up a node with all permissions revoked from Unregistered and Registered, and all permissions given to Admin and Moderating. My account is in both Admin and Moderating groups, and not in the basic Registered. The node does not appear in the forum list and if I open it by direct link it says I have no permission to see it. I can only see it if I allow everyone to view it. It was the same in 1.5.5a and 1.5.6. What am I doing wrong?
That's not the way that permissions should be set up in XenForo. Everyone should have the Registered group as their primary user group and have secondary user groups added to increase permissions (Registered would have the basic permissions that everyone has).
It's going to be difficult to troubleshoot with your current set-up. I suggest you read these permission guides and set your permissions in this way. Hopefully that will then resolve your issues (but if not, it'll be easier to assist).
Indeed. Avoid using Never, you should use Not Set (No) in most cases (so check through your permissions for this). There's only a few cases where Never should be used (for example a 'naughty' user group where you'd set Never permissions to override any Allows set in other user groups).