If you setup some Conditional Forwarders on your DNS servers, you will notice that it won’t propagate any of the domains to other Domain Controllers (eg. Secondary domain controller) by default. You will need to choose the correct option and tell it to propagate to other DCs.

For Windows 2003 DNS servers, you will need to do this at the command prompt.

e.g. dnscmd /ZoneAdd example.com /DsForwarder 192.168.2.3

Click link to see the dnscmd syntax

For Windows 2008 DNS servers, you will need to select the option to use AD integrated zone when creating the conditional forwarders.