This bug is still present in Ubuntu 16.04.

Wireshark's captures show that IPv4 resolvers are preferred to IPv6 resolvers.
It also show the local machine sometimes directly contacting the root server's, 
that's weird.

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https://bugs.launchpad.net/bugs/1002454

Title:
  IPv4 DNS preferred over IPv6 ones

Status in NetworkManager:
  Confirmed
Status in network-manager package in Ubuntu:
  Confirmed

Bug description:
  The Network Manager always prefers IPv4 DNS over IPv6 ones. The issue
  occurs both when DNSs are statically configured and when they're
  acquired via DHCPv4/DHCPv6.

  Network Manager puts IPv4 DNSs before IPv6 ones in the /var/run/nm-
  dns-dnsmasq.conf so Dnsmasq resolves names using IPv4 DNSs before
  using IPv6 ones.

  If I disable Dnsmasq, DNS servers are put in the wrong way in
  /etc/resolv.conf file.

  The system shoud prefer IPv6 DNSs in any case.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: network-manager-gnome 0.9.4.1-0ubuntu2
  ProcVersionSignature: Ubuntu 3.2.0-24.38-generic 3.2.16
  Uname: Linux 3.2.0-24-generic x86_64
  NonfreeKernelModules: nvidia
  ApportVersion: 2.0.1-0ubuntu7
  Architecture: amd64
  CRDA: Error: command ['iw', 'reg', 'get'] failed with exit code 1: nl80211 
not found.
  Date: Mon May 21 21:05:59 2012
  ExecutablePath: /usr/bin/nm-connection-editor
  IfupdownConfig:
   auto lo
   iface lo inet loopback
  InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release amd64 (20111012)
  IpRoute:
   default via 192.168.0.1 dev eth0  proto static 
   169.254.0.0/16 dev eth0  scope link  metric 1000 
   192.168.0.0/24 dev eth0  proto kernel  scope link  src 192.168.0.217  metric 
1 
   192.168.36.0/24 dev vmnet1  proto kernel  scope link  src 192.168.36.1 
   192.168.70.0/24 dev vmnet8  proto kernel  scope link  src 192.168.70.1
  NetworkManager.state:
   [main]
   NetworkingEnabled=true
   WirelessEnabled=true
   WWANEnabled=true
   WimaxEnabled=true
  PciNetwork:
   
  RfKill:
   
  SourcePackage: network-manager-applet
  UpgradeStatus: Upgraded to precise on 2012-05-02 (18 days ago)
  nmcli-con:
   NAME                      UUID                                   TYPE        
      TIMESTAMP    TIMESTAMP-REAL                     AUTOCONNECT   READONLY   
DBUS-PATH                                 
   eth0-Static               0bcb2b9f-a2c0-46f9-a6b1-59f66e383264   
802-3-ethernet    1337627018   lun 21 mag 2012 21:03:38 CEST      yes           
no         /org/freedesktop/NetworkManager/Settings/0
  nmcli-dev:
   DEVICE     TYPE              STATE         DBUS-PATH                         
         
   eth1       802-3-ethernet    unavailable   
/org/freedesktop/NetworkManager/Devices/1  
   eth0       802-3-ethernet    connected     
/org/freedesktop/NetworkManager/Devices/0
  nmcli-nm:
   RUNNING         VERSION    STATE           NET-ENABLED   WIFI-HARDWARE   
WIFI       WWAN-HARDWARE   WWAN      
   running         0.9.4.0    connected       enabled       enabled         
enabled    enabled         disabled

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