The Restart/Shutdown mini-monitor window occurs at a lower level than the code for the USB driver in Mac OS X Server. As a result, USB input is not recognized in this window.
If you have a computer that has a USB keyboard, you should not use the Restart/Shutdown mini-monitor window. Instead you should restart or shut down the server by logging out of Mac OS X Server and clicking the appropriate button. Additionally, Power Macintosh G3 (Blue and White) users can use an Apple ADB keyboard as this issue does not occur with an Apple ADB keyboard.