multiple configuration locations

Scenario: I spend time setting up config.php and then another admin goes and saves something through the admin interface. I come back to the site and see something has changed, I make an adjustment in config.php. Nothing happens. Hair is lost and my computer is brutally insulted.

Configuration entries made through the admin web interface that are stored in the db seem to override those kept in the config.php flat file. This seems contrary to my assumption. In my experience, a flat file with custom config settings will override settings set in-app. At any rate, there needs to be some sort of definite indication as to what overrides what and even better to not have two conflicting configurations in place. There needs to be a way to keep them in sync. Perhaps having the settings from config.php imported into the db when the mod time or sum of the file changes. Or else completely remove one or the other or at least limit the settings that can be done in one or the other so that they each work on a exclusive set of options.