Can you please do a search on your computer for prefs.prop and let me know if there is more than 1 copy of this file? There should only be 1 in your save directory (which you specified above). If you find another in a GameData folder or in your Walking Dead installation directory (steamapps\common\the walking dead), this may be the problem.
Also, can you please answer a few questions? When did you first install the game? Were you prompted for or did you automatically receive any updates when you started Steam? Are you logged into the administrator account on your PC? Do you have Cloudsync enabled? If so, did you receive any error messages from Cloudsync when you started Steam or the game?