You've made me question the DNS setup we have here too.
Our Primary Servers are different but they should be all the same. The reason is the primary server holds the records for that zone and is the authority when it comes to lookups for that zone. If you're primary server doesn't have it then none of the others will. So if each server thinks its the primary server then each will keep its own records and not look to the other servers for records it doesn't have.
If you have more than one domain in your dns you will need to specify the SOA details for each and keep them consistent across the servers.
Have a look here for more info;
http://technet.microsoft.com/en-us/library/cc779148%28WS.10%29.aspx