make sure you have one server set as a primary dns server for all .com (external) zones en active directory integrated for local zones. the other server set local zones ad integrated as well and other zones seconary zones... Make sure you enable "replicate to servers in server name tab" and add your dns servers in the name servers tab.
It sounds like after a dns problem when a server atemps to replicate zones..
This should be the trick.
good luck