It's all very confusing with many people experiencing similar symptoms.
But the original logs look like a simple case of PulseAudio selecting a
far too short latency:

I: protocol-native.c: Final latency 201.00 ms = 0.50 ms + 2*100.00 ms + 0.50 ms
D: alsa-sink.c: Cutting sleep time for the initial iterations by half.
D: alsa-sink.c: Latency set to 0.50ms

And indeed, VLC version 1.1.8 requested tlength=200ms and minreq=100ms.
A similar problem affects more recent VLC versions with tlength=40ms and
minreq=-1 (overriden by PA to 20ms). It seems that when tlength is
exactly twice minreq, PulseAudio settles on an insanely small latency.
That causes frequent underrun in hardware buffers, accounting for the
distorsion.

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https://bugs.launchpad.net/bugs/751265

Title:
  pulseaudio distorts VLC audio

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