Can not RDP to Win 2003 box or initiate remote restart
Solution 1:
Try instead:
shutdown -r -f -m \\hostname -c "Comment goes here"
That's a bit drastic, but I've had the need to do that in a very similar environment to what you describe. I also open a cmd window and start a ping -t against the server to watch when the IP stack goes down and comes back up. This is a very useful indicator of activity when you don't have physical access to the server (or are too lazy to get up and walk over to it).
EDIT: (based on your comment) Ok, do this first and then try the above again (or restart it as normal if this works). See it that gets you farther. The -a will abort a system shutdown.
shutdown -a -m \\hostname
Solution 2:
I encountered the same issue trying to perform a remote reboot on a Windows XP machine. What I ended up doing was using the PsKill command, part of the SysInternals PsTools suite, to kill the Winlogon process, like so:
pskill \\hostname winlogon
This will cause the remote machine to reboot immediately.
Solution 3:
Well, this is kind of crazy but you can enable xp_cmdshell on SQL Server then execute commands as the user that is running SQL Server, so you can do a shutdown -r if it won't listen to remote commands.
If you want to try and re-start RDP w/o rebooting the box, you may try (this is untested; I'm not going to do this on any of my boxes :D):
Figure out what is listening on 3389 (RDP port) by asking for:
xp_cmdshell 'netstat -anO | findstr ":3389"'
Kill the pid with taskkill. Finally, issue a
NET START "TERMINAL SERVICES"
Hold your breath, then try RDP again.