I've heard rumors that Steam might be reverting files back to their original state upon the next run of the installation files. So you change the files, then run steam to play the game, and it reverts the files to what they were before the change, effectively restoring the settings how they were, and deleting your changes. Now, keep in mind, I don't know that to be true, as I haven't tried it, but I've heard some people claim that that is happening.