This can happen when third party, or even Microsoft applications have not properly cleaned up when exiting. Windows will keep trying to unload the profile until Windows finally decides that it can’t and should shutdown. Even if you find the application causing the problem – it may be impossible to do anything about it.

Microsoft released the tool profile hive cleanup because of this. When you install the tool you will find a new service which is called profile hive cleanup service. This service automatically cleans up user profiles when it is running and this should have the result that the shutdown of the system does not take minutes but seconds.

The idea of this program is to reclaim resources when a task is finished (memory, handles, etc). It accomplishes this by monitoring for users to log off and verifying that unused resources are reclaimed. This approach is superior as it works for any known reason that profiles do not unload and also will keep working to address new unknown issues.