Here is how to setup NTP correctly for your domain. I have tested this with Server 2003 and 2008.
On the PDC for the Domain:
w32tm /config /manualpeerlist:"0.north-america.pool.ntp.org 1.north-america.pool.ntp.org 2.north-america.pool.ntp.org 3.north-america.pool.ntp.org" /syncfromflags:manual /reliable:yes /update Net Stop "Windows Time" Net Start "Windows Time" w32tm /resync
If you want to use different servers for peers go to the NTP Pool Project website and select the servers that match your needs. (Don’t forget to put double quotes around your server list and spaces between server names!)
On all the servers and in login scripts:
(This step is technically optional, unless you have previously changed how NTP works on your servers/desktops.)
w32tm /config /syncfromflags:domhier /update
Net Stop w32tm
Net Start w32tm
How do you verify that your PDC has time setup correctly?
From the command prompt run:
w32tm /dumpreg /subkey:parameters
It will output something similar:
Value Name Value Type Value Data ---------------------------------------------------------- ServiceMain REG_SZ SvchostEntry_W32Time ServiceDll REG_EXPAND_SZ C:WINDOWSsystem32w32time.dll NtpServer REG_SZ <peers> Type REG_SZ NTP
The two items you are looking to confirm on your PDC is the Peers match the list you entered and that the Type is set to NTP.
Running the same command on another DC or member server the Type should come back “NT5DS”
Reference:
Configure w32tm on PDC: Microsoft Technet
Configure w32tm on computers: Microsoft Technet