As the title suggests what does "Warning: query response not set" mean. I see the following in the dighost.c (line 2888 and 2889) source but still am uncertain with what in my DNS servers response would cause it.
if (result == ISC_R_SUCCESS && (msgflags & DNS_MESSAGEFLAG_QR) == 0)
printf(";; Warning: query response not set\n");
The QR bit (the MSB in the 3rd octet in the header) indicates whether the packet is a request (0) or a response (1).
All clients MUST therefore send packets with that bit clear, and the server MUST send it back with that bit set. The error messages tell you that a response was received that was flagged as a request.
BTW, there was a known bug in the Microsoft DNS server some years back where it would answer a packet even if the QR bit was set in that packet! As a result it was possible to cause a packet loop.
Looks like this is due to incorrect setting of the QR portion of the response header.