This does indeed look PulseAudio-related. I'm able to reproduce with the
default settings, which outputs to PA, but when I select the ALSA output
module and a proper (hardware) device everything is fine.

It seems to me that there's a buffer issue, especially because of these lines:
[0x195d948] main audio output warning: playback way too early (-398592): 
playing silence
[0x195d948] main audio output debug: inserting 19132 zeroes

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https://bugs.launchpad.net/bugs/1319233

Title:
  audio stutters or stops playing after seeking

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