I also have this problem. I've tried a handful of different ipv6 dns servers to test. Manually specifying the ipv6 address does indeed work fine.
According to this tcpdump, it appears that the AE isn't adding ipv6 addresses to dhcp option 6:
$sudo tcpdump -vvv -s 0 port bootps
(192.168.1.1 is the AE, 192.168.1.2 is a DNS server that I specified, 192.168.1.16 is my MBP)
06:51:19.565546 IP (tos 0x10, ttl 128, id 0, offset 0, flags [none], proto UDP (17), length 328)
192.168.1.1.bootps > 192.168.1.16.bootpc: [udp sum ok] BOOTP/DHCP, Reply, length 300, xid 0x8940e0fa, secs 1, Flags [none] (0x0000)
Your-IP 192.168.1.16
Client-Ethernet-Address my:mac:addr (oui Unknown)
Vendor-rfc1048 Extensions
Magic Cookie 0x63825363
DHCP-Message Option 53, length 1: ACK
Server-ID Option 54, length 4: 192.168.1.1
Lease-Time Option 51, length 4: 86400
Subnet-Mask Option 1, length 4: 255.255.255.0
Default-Gateway Option 3, length 4: 192.168.1.1
Domain-Name-Server Option 6, length 4: 192.168.1.2 <--------- There should be ipv6 addresses here
Domain-Name Option 15, length 21: "mydomain.com"
END Option 255, length 0
PAD Option 0, length 0, occurs 3