The only time I have seen this is when you don't have IPv6 address configured when the setup script is run. You may want to check the setupVars.conf file in the /etc/pihole directory if you see:
IPV4_ADDRESS=192.168.10.250/24
IPV6_ADDRESS=
They you haven't setup IPv6 during the setup. To resolve this run the command.
pihole reconfigure
and make sure when it asks about IP addresses you select IPv6 and it has a static address.
The setVars has the ipv6 address. I don't recall if I added it after or not, but all the variables for ipv6 are set to true/yes - I think. Are there additional things I med to check to make sure they're turned on?
For what it's worth, it does ipv6 dns lookups just fine (lookups over ipv6, and also AAAA lookups), using unbound.
Does that look OK? FWIW the system is responding correctly for dig -6 requests to its IPv6 address. My concern is, not being able to check off additional servers as backups.