The problem is that there are two variables 'TIMEZONE' and 'SERVER_TIMEZONE'.Only one is changed using the WebUI. So you need to login the database manually using phomyadmin and set the timezone correctly on both variables.
mysql> update webcal_config set cal_value="America/Los_Angeles" where cal_setting="TIMEZONE";
mysql> update webcal_config set cal_value="America/Los_Angeles" where cal_setting="SERVER_TIMEZONE";