I am also very interested in a solution to this. Imagine my disappointment when I spent a couple weeks tweaking the site to be exactly how I wanted, go to set it live, and none of my preferences were saved.
For the record I did an export of my entire database from my local installation (MAMP), AND synced my whole WordPress folder, and none of the preferences went to the live site. It boggles my mind where the disconnect is since I have literally copied the entire database and files to the live site. What mysterious place are you storing these preferences in!?
Please notify if there is a fix (that is NOT a paid plugin).