Just like to add I see this problem too. My dnsmasq service starts as
nobody maybe %20 of the time from a cold boot. And dns forwarding is
broken at this time. Killing the process and restarting the service
usually results in the dnsmasq service starting as "dnsmasq" like it
should. But alas still no DNS forwarding and the only  to get it working
again is to reboot.

Not working
nobody    1481  1055  0  7205  1240   0 17:23 ?        00:00:00 
/usr/sbin/dnsmasq --no-resolv --keep-in-foreground --no-hosts --bind-interfaces 
--pid-file=/var/run/sendsigs.omit.d/network-manager.dnsmasq.pid 
--listen-address=127.0.0.1 --conf-file=/var/run/nm-dns-dnsmasq.conf 
--cache-size=0 --proxy-dnssec

Working
dnsmasq   1201     1  0  7205   992   0 17:58 ?        00:00:00 
/usr/sbin/dnsmasq -x /var/run/dnsmasq/dnsmasq.pid -u dnsmasq -r 
/var/run/dnsmasq/resolv.conf -7 /etc/dnsmasq.d,.dpkg-dist,.dpkg-old,.dpkg-new

Xubuntu Server 12.04.2 w/ XFCE
kernel: 3.2.0-45-generic

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https://bugs.launchpad.net/bugs/1105493

Title:
  network manager runs dnsmasq as user nobody

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

Bug description:
  Network Manager starts dnsmasq to provide better performing DNS
  service to the end user; however, it starts dnsmasq as user nobody:

    $ ps auwwx | grep [d]nsmasq
    nobody     993  0.0  0.1  33072  1120 ?        S    12:06   0:00 
/usr/sbin/dnsmasq --no-resolv --keep-in-foreground --no-hosts --bind-interfaces 
--pid-file=/var/run/sendsigs.omit.d/network-manager.dnsmasq.pid 
--listen-address=127.0.1.1 --conf-file=/var/run/nm-dns-dnsmasq.conf 
--cache-size=0 --proxy-dnssec 
--enable-dbus=org.freedesktop.NetworkManager.dnsmasq 
--conf-dir=/etc/NetworkManager/dnsmasq.d

  Generally it's bad form from a security perspective to run daemons as
  user nobody because a vulnerability in one daemon will possibly allow
  it, when compromised, to interfere with another daemon that is also
  running as nobody. The preferred solution is to run it under a
  service-specific system user.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.10
  Package: network-manager 0.9.6.0-0ubuntu7
  ProcVersionSignature: Ubuntu 3.5.0-22.34-generic 3.5.7.2
  Uname: Linux 3.5.0-22-generic x86_64
  ApportVersion: 2.6.1-0ubuntu10
  Architecture: amd64
  CRDA: Error: command ['iw', 'reg', 'get'] failed with exit code 1: nl80211 
not found.
  Date: Fri Jan 25 14:17:36 2013
  IfupdownConfig:
   # interfaces(5) file used by ifup(8) and ifdown(8)
   auto lo
   iface lo inet loopback
  InstallationDate: Installed on 2013-01-25 (0 days ago)
  InstallationMedia: Ubuntu 12.10 "Quantal Quetzal" - Release amd64 (20121017.5)
  IpRoute:
   default via 10.0.2.2 dev eth0  proto static 
   10.0.2.0/24 dev eth0  proto kernel  scope link  src 10.0.2.15  metric 1 
   169.254.0.0/16 dev eth0  scope link  metric 1000
  IwConfig:
   eth0      no wireless extensions.
   
   lo        no wireless extensions.
  MarkForUpload: True
  NetworkManager.state:
   [main]
   NetworkingEnabled=true
   WirelessEnabled=true
   WWANEnabled=true
   WimaxEnabled=true
  ProcEnviron:
   TERM=xterm
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  RfKill:
   
  SourcePackage: network-manager
  UpgradeStatus: No upgrade log present (probably fresh install)
  nmcli-con:
   NAME                      UUID                                   TYPE        
      TIMESTAMP    TIMESTAMP-REAL                     AUTOCONNECT   READONLY   
DBUS-PATH                                 
   Wired connection 1        6065df63-d4a5-4426-bf03-4b938adcdf28   
802-3-ethernet    1359152173   Fri 25 Jan 2013 02:16:13 PM PST    yes           
no         /org/freedesktop/NetworkManager/Settings/0
  nmcli-dev:
   DEVICE     TYPE              STATE         DBUS-PATH                         
         
   eth0       802-3-ethernet    connected     
/org/freedesktop/NetworkManager/Devices/0
  nmcli-nm:
   RUNNING         VERSION    STATE           NET-ENABLED   WIFI-HARDWARE   
WIFI       WWAN-HARDWARE   WWAN      
   running         0.9.6.0    connected       enabled       enabled         
enabled    enabled         disabled

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