I have the exact same problem. I was not sure what it came from at the
beginning but today it was clearly Audacity that stops my headphone port
from working.

I was listening to music before through the same headphones, with different 
apps. As soon as I opened the same sound with Audacity, my headphone port 
stopped working whereas I can unplug them and use my laptop speakers. After 
that, even out of Audacity, I can not use my headphones with the apps that 
worked before then.
I only hear little "breathing" sounds every time a sound/song is supposed to 
start, or when the sound/song is supposed to finish and the app "releases" the 
sound system.

It takes several reboots before it eventually start working again,
sometimes after a few days.

I have no idea what happens but it is an extremely disrupting problem as
I can not make any music without good quality headphones.

I am using Ubuntu 13.10 64bits with Audacity 2.0.5

Please let me know if I can give you something else to help fix this.

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https://bugs.launchpad.net/bugs/1257956

Title:
  Headphones stopped working after use of Audacity. They are detected,
  but no sound is produced.

Status in “pulseaudio” package in Ubuntu:
  Confirmed

Bug description:
  I'm running 13.10 and the latest GNOME. I've just fresh installed
  everything and the problem has occured again the same way. I would
  like to be able to use audacity, but I suppose in the mean time I will
  just reinstall everything. I'm unsure of what outputs I should attach.
  Sorry I'm quite newbish.

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