I just spent a lot of time tracking down an answer to this same problem. Turns out avahi by default doesn't publish an IPv4 A record on IPv6. I added the following line to my /etc/avahi/avahi-daemon.conf:
and restarted avahi-daemon and I could connect to my afp file share from the list in the Finder just fine.
I'm not sure why this was necessary, I installed avahi-utils and looked at the afp shares currently available on the network:
WIthout publish-a-on-ipv6 set to yes, the only record my server was publishing had my IPv6 address. Once I set that option it started publishing my IPv4 address in the address field.
avahi-browse -r _afpovertcp._tcp
I also ran this command from my Mac, which told me the Mac couldn't find an IPv6 record for my fileserver either before or after that change:
dns-sd -G v4v6 servername