I prevented users to make schedule changes of Webalizer by changing config in default server template configuration. Then I ran virtual-server/all_webmin.cgi but still users were able to change Webalizer schedule. The change took place only when I went to Virtual server configuration and saved the config.
I used demo server Virtualmin 3.12. From the thread http://www.virtualmin.com/forums/message-view?message_id=42005 I figured that all_webmin.cgi script should update the changes made to server template but it did not do so.