I’ve found that the Enterprise Mode Site List can also not update if a user logs onto a new PC, with a roaming profile and the Enterprise Mode Site List cache doesn’t roam. Basically what happens is the user logs onto the PC, the registry setting that roams with the user part of the registry (HKCU\Software\Microsoft\Internet Explorer\Main\EnterpriseMode\), but the Site List cache does not. Consequently, after starting IE 11 it checks the registry to see what version of the site list it has, sees that the number matches that of the server and doesn’t download the cache.
To fix this scenario, ensure that you roam the cache with the user’s roaming profile or don’t roam the registry.
This solution is appropriate for users of tools such as Flex+ or Appsense, where an administrator can specify which parts of the profile roam with the user.