I was testing today the same files with the latest CVS moodle 2.0 and noticed that something is not working as it should - javascripts for user preference window did not read variables like they should...either caused by some recent change in cvs or some recent change in my files...
So - if the latest files do not change user preferences it's not your fault... I will check the reason and if necessary upgrade the files as soon as possible.
EDIT: Sorted, I was just trying to use cvs moodle without MathJax files and layout files had script tags for mathJax that had variables for user preferences inside. Now when MathJax did not exist those variables for user preferences were not read either...
