Found a solution. Apparently there is a problem with Pulse Audio on
linux, when you do start/stop too frequently.

http://wiki.audacityteam.org/wiki/Linux_Issues

PulseAudio: Audacity's PulseAudio support generally works well. PulseAudio 
doesn't support ALSA's mixer interface so Audacity's Mixer Toolbar input slider 
is disabled under PulseAudio. Audacity can freeze using PulseAudio if playback 
or recording are started or stopped very rapidly or frequently. Playback can 
also occasionally be distorted or excessively fast. Patches are welcomed to 
improve our PulseAudio support. Meantime a reported workaround for freezes or 
glitched or skipped playback is to launch Audacity from the terminal with the 
following command:
env PULSE_LATENCY_MSEC=30 audacity

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https://bugs.launchpad.net/bugs/792549

Title:
  Audacity freezes when clicking on the audio timeline during playback

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