Sorry for bringing up an old post but I had problems similar to what was
described here.

I was able to "fix" the crackling audio issues using the following lines

high-priority = yes
nice-level = -11
realtime-scheduling = yes
default-fragments = 8
default-fragment-size-msec = 10

Note that this instance of PulseAudio was not running on a ubuntu
machine but on a OpenWRT based router (BT HomeHub 5) which is used as a
sink for a ubuntu based machine - however since this post came high in
the list of search results when I searched the crackling audio issue,
there is a possibility that my addition may help somebody.

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Touch seeded packages, which is subscribed to pulseaudio in Ubuntu.

  Crackling noise after update to pulseaudio

Status in pulseaudio package in Ubuntu:
  Fix Released

Bug description:
  Binary package hint: pulseaudio

  After upgrading to Jaunty, when listening to audio through Pulseaudio,
  I get a crackling sound, that seems to be bound to system load. Not
  necessarily CPU load, the CPU load is well below 50% at all times, but
  I.E. harddisk access seems to provoke the crackling extra.

  When disabling Pulseaudio, running directly towards ALSA, the
  crackling disappear.

  My soundcard according to lspci: nVidia Corporation CK804 AC'97 Audio
  Controller (rev a2). (Motherboard built-in)

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