More research..
OK so I think I've found the source of the problem, but no real idea how to fix it. If I run vlc with -vv I see output such as:
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[00000272] alsa audio output debug: recovered from buffer underrun
[00000272] main audio output debug: audio output is starving (21999), playing silence
[00000272] alsa audio output debug: recovered from buffer underrun
[00000272] main audio output debug: audio output is starving (23425), playing silence
[00000272] alsa audio output debug: recovered from buffer underrun
[00000272] main audio output debug: audio output is starving (21533), playing silence
[00000272] alsa audio output debug: recovered from buffer underrun
[00000272] main audio output debug: audio output is starving (22003), playing silence
[00000272] alsa audio output debug: recovered from buffer underrun
[00000272] main audio output debug: audio output is starving (24374), playing silence
[00000272] alsa audio output debug: recovered from buffer underrun
[00000272] main audio output debug: audio output is starving (22156), playing silence
I also see:
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[00000283] main private debug: looking for audio filter module: 23 candidates
No accelerated IMDCT transform found
Not entirely sure where to look from here.