I did some DNS debugging and noticed that my server wasn’t querying the root-servers via IPv6. I checked the root hint zone file delivered with my Bind9 binary package, the file was from 1998! So I downloaded the latest version from http://www.internic.net/zones/named.root. Of course IPv6 queries to the root-servers work like a charm now, however please note that only 7 of 13 root-servers are IPv6-enabled.