About the last comment: I do not understand very well what's going on.
Here's what I did:

* Before looking at these comments, I removed all wired connections from
network manager configuration. I rebooted the server and the resulting
resolv.conf was not referencing 127.0.0.1 anymore, but the DNS servers
from dhcp directly; I re-added a wired connection from the main adapter
(eth0) with DHCP and the same stuff happened.

* After that I noticed that the dnsmasq package wasn't installed. I
forgot to add the line from ps -ef that showed that dnsmasq was running
as a child process from NetworkManager (I even remember the --no-hosts
parameter) even without the dnsmasq package being there

* I installed dnsmasq just to see what would happen, and the resolv.conf
referencing 127.0.0.1 became active again, and again, it does not work
if I configure my DHCP server to lend it many servers. However, if I
tested with one DNS server and four DNS servers, and both worked OK.

* This "new" dnsmasq process is not a child from NetworkManager and does
not have the file /var/run/nm-dns-dnsmasq.conf - what is going on, does
Networkmanager has a different dnsmasq that comes with it?

* As you can see, before this day I only had dnsmasq-base and not
dnsmasq installed:

[patola@bmw patola]% grep dnsmasq /var/log/dpkg.log
2012-04-06 09:05:34 upgrade dnsmasq-base 2.57-1ubuntu1 2.59-4
2012-04-06 09:05:34 status half-configured dnsmasq-base 2.57-1ubuntu1
2012-04-06 09:05:36 status unpacked dnsmasq-base 2.57-1ubuntu1
2012-04-06 09:05:37 status half-installed dnsmasq-base 2.57-1ubuntu1
2012-04-06 09:05:39 status half-installed dnsmasq-base 2.57-1ubuntu1
2012-04-06 09:05:41 status half-installed dnsmasq-base 2.57-1ubuntu1
2012-04-06 09:05:45 status unpacked dnsmasq-base 2.59-4
2012-04-06 09:05:45 status unpacked dnsmasq-base 2.59-4
2012-04-07 02:19:55 configure dnsmasq-base 2.59-4 2.59-4
2012-04-07 02:19:55 status unpacked dnsmasq-base 2.59-4
2012-04-07 02:19:56 status half-configured dnsmasq-base 2.59-4
2012-04-07 02:19:57 status installed dnsmasq-base 2.59-4
2012-04-30 01:24:28 install dnsmasq <nenhum> 2.59-4
2012-04-30 01:24:28 status half-installed dnsmasq 2.59-4
2012-04-30 01:24:29 status half-installed dnsmasq 2.59-4
2012-04-30 01:24:31 status unpacked dnsmasq 2.59-4
2012-04-30 01:24:32 status unpacked dnsmasq 2.59-4
2012-04-30 01:24:33 configure dnsmasq 2.59-4 <nenhum>
2012-04-30 01:24:33 status unpacked dnsmasq 2.59-4
2012-04-30 01:24:33 status unpacked dnsmasq 2.59-4
2012-04-30 01:24:34 status unpacked dnsmasq 2.59-4
2012-04-30 01:24:34 status unpacked dnsmasq 2.59-4
2012-04-30 01:24:34 status unpacked dnsmasq 2.59-4
2012-04-30 01:24:34 status unpacked dnsmasq 2.59-4
2012-04-30 01:24:34 status unpacked dnsmasq 2.59-4
2012-04-30 01:24:34 status half-configured dnsmasq 2.59-4
2012-04-30 01:24:37 status installed dnsmasq 2.59-4

* I have a central server on my intranet that also does DNS resolution
and caching. Is dnsmasq really needed on this scenario?

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https://bugs.launchpad.net/bugs/991347

Title:
  After upgrade to 12.04 resolvconf seems ok but does not work

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

Bug description:
  I was using a simple scheme for DNS resolution before upgrading from
  11.10 to 12.04: there are three interfaces on the computer, eth0 is
  the main one, acquires IP and DNS automatically from 10.0.0.1, which
  is also the default route.

  But after upgrade to the new DNS scheme on ubuntu 12.04, it does not
  work. Everything seems in order:

  /etc/network/interfaces:
  ------------
  # This file describes the network interfaces available on your system
  # and how to activate them. For more information, see interfaces(5).

  # The loopback network interface
  auto lo
  iface lo inet loopback

  # The primary network interface
  auto eth0
  iface eth0 inet dhcp
  -----------

  /etc/resolv.conf (link to ../run/resolvconf/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 patola.org
  -----------------

  /var/run/nm-dns-dnsmasq.conf:
  ------------------
  server=200.212.223.43
  server=8.8.8.8
  server=8.8.4.4
  server=200.212.223.44
  server=208.53.170.32
  server=200.212.223.100
  server=143.106.2.5
  server=200.162.192.51
  server=200.162.192.50
  server=200.162.192.49
  server=200.162.192.52
  -----------------

  under /etc/resolvconf/resolv.conf.d:
  base - null, 0 bytes
  head:
  ----------------------------
  # 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
  --------------------------

  original:
  -----------------------
  # Generated by NetworkManager
  domain patola.org
  search patola.org
  nameserver 200.212.223.43
  nameserver 8.8.8.8
  nameserver 8.8.4.4
  # NOTE: the libc resolver may not support more than 3 nameservers.
  # The nameservers listed below may not be recognized.
  nameserver 200.212.223.44
  nameserver 208.53.170.32
  nameserver 200.212.223.100
  nameserver 143.106.2.5
  nameserver 200.162.192.51
  nameserver 200.162.192.50
  nameserver 200.162.192.49
  nameserver 200.162.192.52
  ---------------------

  In other words, all these server are the right ones, however, when I
  try to do a DNS query, it goes like that:

  [root@bmw ~]# dig www.terra.com.br

  ; <<>> DiG 9.8.1-P1 <<>> www.terra.com.br
  ;; global options: +cmd
  ;; Got answer:
  ;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 53771
  ;; flags: qr rd ra; QUERY: 1, ANSWER: 0, AUTHORITY: 4, ADDITIONAL: 6

  ;; QUESTION SECTION:
  ;www.terra.com.br.            IN      A

  ;; AUTHORITY SECTION:
  terra.com.br.         71303   IN      NS      d.dns.terra.com.br.
  terra.com.br.         71303   IN      NS      b.dns.terra.com.br.
  terra.com.br.         71303   IN      NS      a.dns.terra.com.
  terra.com.br.         71303   IN      NS      c.dns.terra.com.

  ;; ADDITIONAL SECTION:
  d.dns.terra.com.br.   70276   IN      A       200.215.194.1
  d.dns.terra.com.br.   70276   IN      AAAA    2001:12c0:0:2151:200:154:46:21
  b.dns.terra.com.br.   70276   IN      A       200.215.193.1
  b.dns.terra.com.br.   70276   IN      AAAA    2001:12c0:0:2151:200:154:46:20
  a.dns.terra.com.      156677  IN      A       200.215.193.1
  c.dns.terra.com.      156677  IN      A       200.215.194.1

  ;; Query time: 17 msec
  ;; SERVER: 127.0.0.1#53(127.0.0.1)
  ;; WHEN: Sun Apr 29 15:05:37 2012
  ;; MSG SIZE  rcvd: 235

  In other words, it returns a null response!!! No address!

  As soon as I change 127.0.0.1 on /etc/resolv.conf to a real DNS
  server, it works again. But of course, when configured this way it
  never uses dnsmasq. Why has the conversion not worked?

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: resolvconf 1.63ubuntu11
  ProcVersionSignature: Ubuntu 3.2.0-24.37-generic 3.2.14
  Uname: Linux 3.2.0-24-generic x86_64
  NonfreeKernelModules: nvidia
  ApportVersion: 2.0.1-0ubuntu6
  Architecture: amd64
  Date: Sun Apr 29 14:46:00 2012
  InstallationMedia: Ubuntu 11.04 "Natty Narwhal" - Release amd64 (20110426)
  PackageArchitecture: all
  SourcePackage: resolvconf
  UpgradeStatus: Upgraded to precise on 2012-04-06 (23 days ago)

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