IgNiTeD SoUL

Issue: We had a System running Server 2008 and when it would boot it would hang with “Applying User Settings”.  When it would finally load, many of the services were not started.
Diagnosis: http://support.microsoft.com/kb/2004121 – This Microsoft Article explains the issue associated with the SCM database being locked:

sc querylock
The output below would indicate that the SCM database is locked:
QueryServiceLockstatus – Success
IsLocked : True
LockOwner : .\NT Service Control Manager
LockDuration : 1090 (seconds since acquired)
Resolution: You can modify the behavior of HTTP.SYS to depend on another service being started first.  To do this, perform the following steps:

1. Open Registry Editor
2. Navigate to HKLM\SYSTEM\CurrentControlSet\Services\HTTP and create the following Multi-string value: DependOnService
3. Double click the new DependOnService entry
4. Type CRYPTSVC in the Value Data field and click OK.
5. Reboot the server

NOTE: Please ensure that you make a backup of the registry / affected keys before making any changes to your system.