Yes, its a binary file in one of the $HOMEDIR/.gnome<something> directories. Unless you completely understand how to edit it... it will possibly make you unable to login. Best just use the features already given to you to modify it.
Maybe you have permissions wrong for some files. Like, you launched something by root, file got owner root, and now it can't be written on logout. try in console chown -R user ~ where "user" is your username Regards, Atis