Hello Thomas, so a little while ago (maybe 3 weeks) there was an update
to the resolvconf package, which mysteriously changed
/run/resolvconf/resolv.conf to use 127.0.0.1 as the DNS server, along
with a correct search domain.

Initially, when I was connecting to a network and specified DHCP for the
address, but a manually entered DNS record, the resolv.conf would
directly point to the DNS server I specified rather than localhost. The
behavior appears to have changed.

I'll check on my school network whether this is still an issue, so
tomorrow in other words.

Incidentally, I should mention that nm-applet is a little wonky.
Sometimes it stops updating the list of available APs, and I have to run
"killall nm-applet" then run nm-applet for it to work properly. On
occasion this happens twice within a single session, but generally every
other time I resume my computer after it is suspended. Browsing the
internet stops working, my connection to an 802.1x authenticated network
won't work, etc until I respawn nm-applet.

File a new bug?

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Packages, which is subscribed to network-manager in Ubuntu.
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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