Something in the recesses of my memory wants to say that this is one of the numerous issues that can come about from the faulty IDE headers (cold solder joints). I seem to remember it being reported before and thinking that it was odd that the IDE header could affect music playback in that way.

Then again, perhaps my memory is just rubbish.

Wouldn't hurt to check it carefully though. Both of the units I had eventually developed problems with the IDE headers.

Do you have a tuner? Does the same sound occur over tuner (or AUX input?)