I disabled IPv6 on my home network completely because it interferes with my use of my Raspberry Pi as a DNS blocker. I was never able to get DNS working properly, which, apparently, is intentional with regards to the IPv6 protocol.
Your problem was having a non-Pi-hole DNS server configured. If you want to run all of your DNS queries through Pi-hole, don't configure a DNS server that's not the Pi-hole server (or which doesn't forward its queries to it).
It's not supposed to. My pihole blocks IPv6 just fine, whether it's being reached from an IPv4 or an IPv6 address. IPv6 has very little to do with DNS.
Meh.