If you're rebooting a server, and you notice it gets stuck at "Windows is shutting down...", this article may help you. In this case, the server continued to operate normally, however, if you use remote desktop or psexec.exe to connect to the system to reboot it, you'll see something like this:

To fix this issue, I used the pskill.exe utility from the sysinteranls suite to kill the winlogon.exe process. Download pskill.exe from here onto another system on the network, then run the following command:

pskill.exe \\server-name winlogon.exe

The server should begin to reboot like normal now.