Just after doing an Active Directory migration to Windows 2008 R2 native mode I started experiencing odd DNS registration behaviour. The DNS for this domain is hosted in AD, so the migration meant that all DNS servers were now 2008 R2 (replacing 2003 R2). As a result, some 2008 R2 member servers decided to register IPv6 addresses for their automatic 6to4 tunnel interfaces in DNS which led to connectivity problems for clients (which are all Windows 7, and therefore IPv6 aware). What was really strange is that this was not consistent. Some servers were unaffected, despite being in the same subnet.
The workaround was to disable all IPv6 tunnelling over IPv4. Here are the netsh commands since they vary enough to be confusing…
netsh interface ipv6 6to4 set state state=disabled netsh interface ipv6 set teredo type=disabled netsh interface ipv6 isatap set state state=disabled
netsh interface ipv6 6to4 show state netsh interface ipv6 show teredo state netsh interface ipv6 isatap show state