Yeah, we are using this on alot of sites - this one being one of them - and it really hasn't changed that much over the years. My guess is you are missing something.
Don't delete the fifth mail config option - that's used by UBB.Threads 6.3.
Are you seeing those other 2 config options in that extra area as well ? Or are those gone each time you go back to the config file? My thought being if your config file isn't writable - the changes aren't getting saved.
