2000 Server handles powering off differently then 98 did. First and foremost, it is necessary for the computer to enter that state of waiting to shutdown since it needs that time to close any and all of it's open files. Plus, allows any services running to stop correctly. Win98 actually had a bug in it that a patch was suppose to fix that slowed the shutdown process before the ATX power supply turned off.
Is there a UPS attached to the server now as well? This also may stop the system from powering off too soon or at all.
Ben Eric