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

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