One of my least favorite, and recurring, issues with Windows is one that pops up all the time where you try to reboot a server while you are in a remote desktop session; the RDP session will end but the server never reboots.  In my experience this only happens when you reboot within a normal RDP session, but if you are logged in with the /console or /admin switch it will work fine.  This fix is relatively old, but it is one that is not talked about very frequently.  This can also happen if you are logged into a regular RDP session and are trying to run Windows Updates.

This problem is a result of deadlocks occurring between the NTFS shutdown process and disk resource access.  Usually, your server will remain online responding to ping when this happens, and you can even get into computer management, remote registry, and other things remotely.  Getting back into the server through RDP however does not work because terminal services is already shutting down.  You can read more about this at the link below for the KB article.

Without this fix your options are limited to bring the server down gracefully, in fact many people would just do a hard reset from the power button to finish the reboot.  You can however issue a remote shutdown command from the command line.  Simply run “shutdown /r /t 5 /m \\computer_name” without the quotes to reboot the machine in question.  Make sure you don’t forget the /m switch otherwise you will end up rebooting your own machine.  /t is for the time to wait before shutting down and you can use 0 if you like to shutdown immediately, but this doesn’t give you a chance to send an abort (/a) if you enter the wrong server accidentally. You can also issue “shutdown /i” without the quotes to get the interactive dialog which will let you enter a list of servers to reboot and a few other options.

The Microsoft patch for this can be acquired from the following page: http://support.microsoft.com/kb/930045

Note: This does not solve the problem every single time.  I have seen the issue occur even after applying this patch, but it seems to fix the problem for the vast majority.