Here’s how to prevent Automatic Update from rebooting your machine:

</p>

  1. Start -> Run
  2. Type: gpedit.msc
  3. Expand Local Computer Policy / Computer Configuration / Administrative Templates / Windows Components / Windows Update
  4. Double-click “No auto-restart for scheduled Automatic Updates installations”
  5. Select “Enabled”, then OK. Close the Group Policy configuration
    program.

Fine print: 

</p>

  1. You need Administrator priveleges to make this setting.

  2. Some people complained that Windows ignored the “no auto-restart” setting for the WMF patch. Potentially a ID 10T error, though. 

From [JonGalloway.ToString()]

In the comments, there was another good tip for Windows Server 2003: Under Administrative Templates / System right-click on “Display Shutdown Event Tracker” and select properties. Select Disabled to prevent Windows from asking for a reason why you are shuting down Win2003 Server.