Consider the following scenario: A user has a Windows client running UE-V (User Experience Virtualization) and IE 11 and everything in regards to Enterprise Mode in Internet Explorer 11 is working fine. The user then gets a new machine or logs into another machine let it be a client or for instance Remote Desktop session and then Enterprise Mode in IE11 does not work at all. The URL:s defined in the Enterprise Mode XML ruleset file are not applied when the user browse a web application defined for Enterprise Mode.
The problem is a consequence of UE-V roaming the Enterprise Mode registry key HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Main\Enterprise Mode where it lists CurrentVersion with the current version of the XML file that is being used. So basically that means that Enterprise Mode think it has already applied the current ruleset although it has not.
Solution / Workaround
The workaround to prevent this scenario from happening is to exclude that registry key from being roamed. In the MicrosoftInternetExplorer2013.xml file scroll down to <Application> <Name>Internet Explorer 11</Name> and add an additional exclusion to the other exclusions already listed under <Registry>:
For users that are already affected by the problem one must delete the registry key mentioned above and make sure that it is not synced back from the IE package in the SettingsPackages location (MicrosoftInternetExplorer.Version11 package).