Ah, you hadn't mentioned before that the auto setting is becoming unchecked. That does change things a bit, and does lend some credence to a problem app. I don't recall seeing anywhere here of an app that was causing that problem, but I couldn't claim to have memorized all the problems seen here.
If you can, go through your apps and see if there is one (or more) that controls the screen brightness independently of how the phone is set. I know that Aldiko has a setting like that, I'm sure there are others. Or put the setting on auto, then load and unload all of your most used apps. In between each app check the auto setting, maybe that way you'll be able to find the offender.