To ensure a restart on a Windows 2003 machine you can use the following command line syntax:
Example Code - Restarting Windows from the command line
C:\>shutdown /r /t 0 /f
Each of the options in the command above represent the following options:

• /r - Restart the server
• /t xxx - Time to delay before restarting the server
• /f - Performs a forced shutdown and ungracefully shuts down any programs even if they are in the middle of processing