Hmm. Strange. I wonder if something in your settings is bugged out. I'm not necessarily suggesting you do this, just bringing it up. A lot of times when I have issues with an app, I'll go into Manage Apps and Clear Data, Defaults, Cache, etc., and sometimes that can fix the problem. I went into Manage Apps, and, all I have for Settings is Clear Data. That option made me VERY nervous. I assume it would also clear out all of your settings, like, Sounds, Accounts, etc. But, I really have no idea. It's only something I would probably end up trying as a last resort, and, I would assume it'd have some type of ramifications that would make me unhappy. And, I definitely wouldn't take that risk just to fix a problem with my screen brightness. And, before I even tried anything like that, I would definitely do some research to see exactly what Clearing Data on Settings would do.
Maybe someone else will have more insight on your problem.
Personally, I like the job my phone does with Automatic Brightness.