In an environment we have a legacy GPO that has an automatic configuration script defined in Internet explorer maintenance.
In this same environment, we created a new GPO that uses group policy preferences to set the proxy settings.
In this configuration, it takes a user to log on twice before the GPO with the group policy preferences takes precedence.
Note: IEM is not in preference mode. See technet article below.
So today we removed the automatic configuration from the legacy GPO and there was a couple of issues
users still had to log in twice
the proxy settings check box for internet explorer proxy settings kept un-checking itself