The DNS Server service in Windows Server 2008 has a bug that can result in a large number of DNS records disappearing. When those records go missing, you will start seeing problems with anything that depends on name resolution, which in an Active Directory environment is pretty much everything. Note this hotfix only applies to standard secondary zones. Active Directory-integrated zones are not affected by this issue because they use AD replication, not zone transfers, to stay synchronized.
Microsoft has issued a security update KB953317, A primary DNS zone file may not transfer to the secondary DNS servers in Windows Server 2008.