If you are running into issues with unexpected “Pending Reboot” status on a Windows box it’s worth while to check the following key:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager should contain a key named “PendingFileRenameOperations” which is a REG_MULTI_SZ key. This contains the pointers to all files currently being updated. This key can, in some cases, get poluted by installs that went bad.
As always with RegKeys, be carefull and make backups of anything you remove or change.