Other notes:
    * dig always resolves correctly, no router's address prepended.

Could you share your dig command and output please.

Sure. Let's try www.sun.com, for example:

        $ dig www.sun.com

        ; <<>> DiG 9.6.1-P3 <<>> www.sun.com
        ;; global options: +cmd
        ;; Got answer:
        ;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 193
        ;; flags: qr rd ra; QUERY: 1, ANSWER: 1, AUTHORITY: 4, ADDITIONAL: 0

        ;; QUESTION SECTION:
        ;www.sun.com.                   IN      A

        ;; ANSWER SECTION:
        www.sun.com.            740     IN      A       137.254.16.57

        ;; AUTHORITY SECTION:
        sun.com.                51047   IN      NS      ns1.sun.com.
        sun.com.                51047   IN      NS      ns2.sun.com.
        sun.com.                51047   IN      NS      ns8.sun.com.
        sun.com.                51047   IN      NS      ns3.sun.com.

        ;; Query time: 1 msec
        ;; SERVER: 2002:5f52:81a4:1::1#53(2002:5f52:81a4:1::1)
        ;; WHEN: Fri Jun 25 16:31:47 2010
        ;; MSG SIZE  rcvd: 117


        $ dig www.sun.com AAAA

        ; <<>> DiG 9.6.1-P3 <<>> www.sun.com AAAA
        ;; global options: +cmd
        ;; Got answer:
        ;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 1994
        ;; flags: qr rd ra; QUERY: 1, ANSWER: 0, AUTHORITY: 1, ADDITIONAL: 0

        ;; QUESTION SECTION:
        ;www.sun.com.                   IN      AAAA

        ;; AUTHORITY SECTION:
        sun.com.                892     IN      SOA     ns1.sun.com. 
hostmaster.sun.com. 2010062402 3600 1200 1038800 900

        ;; Query time: 5 msec
        ;; SERVER: 2002:5f52:81a4:1::1#53(2002:5f52:81a4:1::1)
        ;; WHEN: Fri Jun 25 16:50:37 2010
        ;; MSG SIZE  rcvd: 80


Now ping is wrong, as already mentioned:

        $ ping -a www.sun.com
        www.sun.com (2002:5f52:81a4:1::1) is alive
        www.sun.com (137.254.16.57) is alive

    * Linux and FreeBSD work fine with IPv6 on the same connection.

Do they use the same nameserver in /etc/resolv.conf?

Yes.

Capture what's happening on the network as you make the requests using
snoop or wireshark.

Tried that with ping -a www.sun.com

* ping asked for www.sun.com AAAA and received an empty response.
* ping asked for www.sun.com.podzimek.org (!!!) and received the address of my 
router (which explains a lot).
* ping asked for www.sun.com A and received 137.254.16.57.
* ping sent/received ICMPv6 and IPCMv4 packets.

The conversation is attached as ping.pcap.

I don't know how the 'www.sun.com.podzimek.org' domain is constructed. I don't 
have any 'search' line in /etc/resolv.conf, as already mentioned.

My /etc/defaultdomain file contains 'helium.podzimek.org'. I don't know if this 
is related to host name resolution or not. The installer created that file and 
I have never touched it. Anyway it's the only file containing 'podzimek.org' in 
the whole /etc directory. :-)

Andrej

Attachment: ping.pcap
Description: Binary data

Attachment: smime.p7s
Description: S/MIME Cryptographic Signature

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