I have this same problem, also on Ubuntu 9.10 amd64. This is version 1.02 from 
the repositories. For me it seems to be more like every 2 seconds but sometimes 
it's very noticeable and sometimes just very faint pops. Occasionally it won't 
happen but then it does  when I try the same file again later or it'll just 
start as I'm listening to it.
Everything else as above, all other audio and video players are fine, and it 
happens whatever audio setting is used.

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VLC sound light stuttering every few seconds (pulseaudio, alsa, oss) (video or 
music file)
https://bugs.launchpad.net/bugs/479868
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