I looked at this carefully; and wrote a (I hope) pretty complete blog post 
explaining the situation:
http://blog.cyphermox.net/2012/08/bug-1010724-why-doesnt-dnsmasq-listen.html

I'll mark prioritize this down to Wishlist for now, since there doesn't
in fact appear to be lag caused by the current setup. It's going to be
something to revisit later should there be time to look into the
situation, but I'm not going to worry too much about it unless there's
clearly an issue.

This is just a prioritization for the development work on NetworkManager
by Ubuntu developers maintaining the package. It basically just means
that *I* won't spend time looking into the situation further, but I'll
be happy to sponsor patches should someone come up with a clever way to
cover all the issues I noted in the above blog entry; namely:

- It should show up in /etc/resolv.conf; but that also seems like unnecessary 
duplication of information.
- Starting dnsmasq entries on ::1 may cause issues with other dnsmasq instances.

It was brought to my attention that draft-smith-v6ops-larger-ipv6
-loopback-prefix-00 aims at fixing this, but it's going to take a while
and lots of work for these solutions to be accepted and implemented.

** Changed in: network-manager (Ubuntu)
   Importance: Low => Wishlist

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https://bugs.launchpad.net/bugs/1010724

Title:
  NM fails to start dnsmasq such that it listens on ::1

Status in “network-manager” package in Ubuntu:
  Triaged

Bug description:
  I have IPv6 activated on Ubuntu 12.04 LTS and I receive an IPv6
  address through DHCPv6. However, requests sent through IPv6 fail. For
  example:

  strainu@emily:~$ dig aaaa -6 google.com

  ; <<>> DiG 9.8.1-P1 <<>> aaaa -6 google.com
  ;; global options: +cmd
  ;; connection timed out; no servers could be reached

  But:

  strainu@emily:~$ dig aaaa google.com

  ; <<>> DiG 9.8.1-P1 <<>> aaaa google.com
  ;; global options: +cmd
  ;; Got answer:
  ;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 60426
  ;; flags: qr rd ra; QUERY: 1, ANSWER: 1, AUTHORITY: 4, ADDITIONAL: 4

  ;; QUESTION SECTION:
  ;google.com.                  IN      AAAA

  ;; ANSWER SECTION:
  google.com.           94      IN      AAAA    2a00:1450:400d:805::1000

  
  Looking into /etc/resolv.conf, I see:

  strainu@emily:~$ cat /etc/resolv.conf 
  # Dynamic resolv.conf(5) file for glibc resolver(3) generated by resolvconf(8)
  #     DO NOT EDIT THIS FILE BY HAND -- YOUR CHANGES WILL BE OVERWRITTEN
  nameserver 127.0.0.1
  search lan

  And with netstat:

  strainu@emily:~$ netstat -ln
  Active Internet connections (only servers)
  Proto Recv-Q Send-Q Local Address           Foreign Address         State     
 
  tcp        0      0 127.0.0.1:53            0.0.0.0:*               LISTEN    
 
  tcp        0      0 127.0.0.1:631           0.0.0.0:*               LISTEN    
 
  tcp6       0      0 ::1:631                 :::*                    LISTEN    
 
  udp        0      0 127.0.0.1:53            0.0.0.0:*                         
 
  udp        0      0 0.0.0.0:68              0.0.0.0:*                         
 
  udp        0      0 0.0.0.0:5353            0.0.0.0:*                         
 
  udp        0      0 0.0.0.0:38399           0.0.0.0:*                         
 
  udp6       0      0 :::47973                :::*                              
 
  udp6       0      0 :::5353                 :::*          

  Apparently, the local dnsmasq server does not listen on IPv6, which is
  wrong. The server should also listen on ::1:53, to allow IPv6-only
  connections. Alternatively, the resolvconf package should write the
  actual DNS server received through DHCPv6 in /etc/resolv.conf

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: resolvconf 1.63ubuntu14
  ProcVersionSignature: Ubuntu 3.2.0-24.39-generic 3.2.16
  Uname: Linux 3.2.0-24-generic x86_64
  ApportVersion: 2.0.1-0ubuntu8
  Architecture: amd64
  Date: Sat Jun  9 02:27:02 2012
  InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release amd64 (20111012)
  PackageArchitecture: all
  SourcePackage: resolvconf
  UpgradeStatus: Upgraded to precise on 2012-05-28 (11 days ago)

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