There is a known issue that can sometimes arise with DNS resolution and IPv6 Records. It manifests itself as DNS problems occurring for certain domains from specific nodes. The IP version used to transport the DNS queries and responses is independent of the records being queried; AAAA records might be queried over IPv4 and A records over IPv6. The problem arises when a domain has both A and AAAA NS records, the A records expire before the AAAA records, and the DNS server that is making the queries is on IPv4 only. When this happens the resolver gets stuck; it cannot query any NS server for the domain, so it times out. This impacts both web and DNS tests, as our DNS experience does not try to resolve the NS entries (it simply uses what the local DNS cache has). Typically this does not happen, but in some cases, people might have different TTL specified for the NS servers in different zones.
The following example illustrates a scenario where the cache had only IPv6 entries for pdns1, pdns2, pdns3, and pdns4.
We utilize Microsoft DNS Server as a recursive resolver and have raised the issue with Microsoft. The official answer from Microsoft is that they are following the RFC, and the issue is with the DNS administrators of such zones. However, they are looking at potentially enhancing their server to solve it elegantly, but there is no ETA for this. Our engineers have been looking into how to solve this internally for the short term, but we cannot provide an ETA. You can read more about this in the following RFC: http://tools.ietf.org/html/rfc4472