Question: Why did everything work on your machine when standalone
dnsmasq wasn't in bind-interfaces mode but /etc/NM/NM.conf contained
"dns=dnsmasq"?

Hypothesis: Standalone dnsmasq started first; network-manager second. NM
tried to start NM-dnsmasq but this failed because of the address
conflict and NM fell back to non-dnsmasq mode, which works fine. If this
hypothesis is correct then there may be lines in the syslog that look
like this:

   [date] [hostname] NetworkManager[pid]: <info> DNS: starting dnsmasq...
   [date] [hostname] dnsmasq[pid]: failed to create listening socket for 
127.0.1.1: Address already in use

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Packages, which is subscribed to network-manager in Ubuntu.
https://bugs.launchpad.net/bugs/959037

Title:
  NM-controlled dnsmasq prevents other DNS servers from starting

Status in “djbdns” package in Ubuntu:
  Confirmed
Status in “dnsmasq” package in Ubuntu:
  Fix Released
Status in “network-manager” package in Ubuntu:
  Fix Released
Status in “pdns-recursor” package in Ubuntu:
  Invalid
Status in “pdnsd” package in Ubuntu:
  Invalid
Status in “djbdns” source package in Precise:
  Confirmed
Status in “dnsmasq” source package in Precise:
  Triaged
Status in “network-manager” source package in Precise:
  Triaged
Status in “pdns-recursor” source package in Precise:
  Invalid
Status in “pdnsd” source package in Precise:
  Invalid

Bug description:
  As described in
  https://blueprints.launchpad.net/ubuntu/+spec/foundations-p-dns-
  resolving, network manager now starts a dnsmasq instance for local DNS
  resolving.

  That breaks the default bind9 and dnsmasq installations, for people that 
actually want to install a DNS server.
  Having to manually comment out "#dns=dnsmasq" in 
/etc/NetworkManager/NetworkManager.conf doesn't sound good, and if it stays 
that way, it should be moved to the bind9 and dnsmasq postinst scripts.

  Please make network-manager smarter so that it checks if bind9 or
  dnsmasq are installed, so that it doesn't start the local resolver in
  that case.

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