We've got a 2 domain controllers on Windows 2008 R2 (migrated from 2003). Replication works fine and everything seems to work just fine but we noticed one of DC's (and DNS for that matter) seems to ignore Conditional Forwarders for our test domains and it directly ask Internet DNS so it gets different values then it should. Each DC points to each other and itself only and they have set Forwarders set to 126.96.36.199 and 188.8.131.52. Conditional forwarders are set to some local IP addresses.
I've seen this kind of of problem for 2003 (http://support.microsoft.com/kb/953419/en-us) but it doesn't seem to mention 2008 R2.