Theres a few of these in the event log - but I presumed this was just a side effect of windows shutting down ?

Event Type: Warning
Event Source: Userenv
Event Category: None
Event ID: 1517
Date: 08/09/2004
Time: 07:48:04
User: NT AUTHORITY\SYSTEM
Computer: THECLAP
Description:
Windows saved user THECLAP\MrHappy registry while an application or service was still using the registry during log off. The memory used by the user’s registry has not been freed. The registry will be unloaded when it is no longer in use.

This is often caused by services running as a user account, try configuring the services to run in either the LocalService or NetworkService account.