I just tried to reproduce this in Ubuntu 12.10 but could not.

I clicked  "Network | Edit Connections..." to open "Network
Connections". I selected the "Wireless" tab and selected a non-active
connection name. I clicked "Edit..." to open "Editing <connection-
name>". In the "IPv4 Settings" tab I set "Method" to "Automatic (DHCP)
addresses only"; I entered address "8.8.8.8" in the "Additional DNS
servers" field; I entered a domain name in the "Search domains" field
and clicked "Save..."  The search domain name and address did not appear
in /etc/resolv.conf, even after I restarted network-manager.

Andrew, are these the same steps you took?

Also, are you sure that you did not at some point add the search domain
name and nameserver address to /etc/network/interfaces or to one of the
files in /etc/resolvconf/resolv.conf.d/?


** Changed in: network-manager (Ubuntu)
       Status: New => Incomplete

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https://bugs.launchpad.net/bugs/1050721

Title:
  Nameserver address entered for one connection gets added to
  resolv.conf for all connections

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

Bug description:
  Hello, I have several WiFi networks with the option "saved for all
  users" enabled on my laptop, meaning the config files are written to
  /etc/NetworkManager. I use DHCP on all these networks, but one of them
  has a misconfigured AP that assigns an incorrect DNS server; I've set
  that one network to assign addresses only via the connection editor,
  and inserted the required DNS info myself for said connection.

  Here's the problem: my /etc/resolv.conf adds this manually added DNS
  server and the search domain in front of any and all other DNS servers
  that dhcp provides no matter what other network I've connected to.
  This basically breaks my DNS.

  I'm running 12.04.1 LTS on a 64-bit machine, no mods to the system or network 
stack, pretty much a pristine install. 
  Network manager is 0.9.4.0-0ubuntu4.1

  If there are any tests or info you'd like, please let me know.

  Here is a copy of resolv.conf while connected to a network whose DNS
  is supposed to be the router (192.168.2.1), edited for privacy:

  # 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 134.74.***.***
  nameserver 192.168.2.1
  search ccny.cuny.edu local

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