The change suggested in this report was in fact implemented for 12.04
but it gave rise to bug #1003842.

Thus for the sake of performance improvements under unusual
circumstances, some users experience inability to resolve private domain
names under circumstances that are not uncommon.

My personal opinion is, therefore, that the change made here should be
reverted until such time as a better solution is found for bug #1003842.
But we can continue the discussion in #1003842.

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https://bugs.launchpad.net/bugs/903854

Title:
  Change default dnsmasq flags to not include --strict-order and disable
  caching

Status in “network-manager” package in Ubuntu:
  Fix Released

Bug description:
  When using dnsmasq as a backend, Network Manager currently passes
  --strict-order.

  This is a good way to get a similar behaviour to that of the libc's
  resolver where the DNS servers are being queried sequentially with a
  2-3s timeout per server. However in the case where the first DNS
  server is down, this will delay all the DNS queries on the system.

  Instead, I recommend this parameter be dropped which will fallback to
  the default dnsmasq mode to send the initial request to all servers
  and then continue with the first one that replies. This will increase
  the load on the upstream DNS servers quite a bit (though not as much
  as using --all-servers) but will ensure a proper fallback when some
  servers are down or very slow.

  I think this added load is reasonable and shouldn't affect most DNS
  servers too much. For cases where it's a concern (heavily loaded
  corporate network for example), I'd suggest the user simply turns off
  the dnsmasq plugin in /etc/NetworkManager/NetworkManager.conf thereby
  reverting to the libc's behaviour of trying servers sequentially with
  a 3s timeout.

  
  As discussed in 
https://blueprints.launchpad.net/ubuntu/+spec/foundations-p-dns-resolving for 
security reason (possible local cache poisoning), we also want to turn off 
caching for the LTS and reconsider caching (ideally with per-user caches) for 
12.10.

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