Not sure if this information is useful but... I continued to play with
Audacity and Pulseaudio. I turned off "Software Playthrough" and that
did not fix the problem. It still only worked at 96Khz and 48Khz. I
installed "PulseAudio Device Chooser". I took a look at the sinks and
sources, opened the volume meters but did not change any settings. When
I went back to Audacity, it was now working, recording at any sample
rate. So I turned "Software Playthrough" back on in Audacity and now
nothing records. Cant record at any sample rate. I then turned off
"Software Playthrough" again and now nothing records at any sample rate.
Nothing plays either. So at this point it is broken completely.

After playing with the various settings here is how I got 
it to work (more or less):

Applications-Sound & Video-Audacity
  Toolbar:
    Output Volume - max
    Input Volume - max, Capture:1
  Edit-Preferences-Audio I/O:
    Playback - (hw:0,0)
    Recording - (hw:0,2)
    Playthrough -
      Uncheck Overdub
      Uncheck Software Playthrough

Volume Icon-Volume Control
  Device: (ALSA Mixer)
  Playback:
    UnMute (and max volume) - Master, PCM, Front, Mic Boost
    Mute - Line-in, CD, Mic, PC Speaker
  Recording:
    Capture:
      Unmute Speaker
      Mute Mic
    Capture 1
      Mute Speaker
      Unmute Mic
    Switches:
      Check - Headphone
      Uncheck - IEC958, IEC958 Capture, IEC958 Default PCM
    Options:
      Channel Mode - 2ch
      Input Source - Line
      Input Source - Mic
    Sound Theme:
      Default

Other comments:
- Re-activating software playthrough works (sometimes). So I don't think this 
  bug is specific to using software playthrough. 
- Changing the input source on the audacity toolbar does not change 
  the recording input.
- Changing the Volume Control options will change the recording input 
  but it works intermittently. Sometimes the change happens and 
  sometimes it does not.
- The output and input volume controls on Audacitys toolbar does not 
  work (volume stays the same regardless of control setting)
- The PulseAudio Volume Meter does not work when Audacity is 
  playing (works with other apps)
- Sample rates 96kHz, 48kHz, 44kHz work, 22kHz, 16kHz, 8kHz do not 
  work (stops after 1 sec. recording). 
- Sometimes all rates work but I was never able to constantly get it 
  back to where all sample rates worked.

-- 
audacity stops recording after about a second when using software play-through
https://bugs.launchpad.net/bugs/355846
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