Our Windows 2003 Server refused to sync the clock via NTP. Main reason for this behaviour is the fact that as PDC it wants to change the NTP server’s clock as well, which is normally not permitted by the NTP server and the packet is discarded.
To change the preferred server of the Windows Time service (w32time), follow these steps:
w32tm /config /manualpeerlist:<server>,0x8 /syncfromflags:MANUALw32tm /config /update
net time /querysntp
w32tm /resync
(source: Meinberg Funkuhren – FAQ – Windows synchronisiert nicht mit NTP (German))