If Im understanding you correctly, the users profile who is logging in, is not keeping the changes you made on the template. Give this link a try: http://www.standalone-sysadmin.com/blog/2009/07/changing-the-windows-xp-default-user-profile/
You make a change on an un-privileged user. Then log in as an admin, and copy that unprivileged users profile to the default users profile.
This should make all of your settings (registry and all) stick.