OT unwanted noises only in iTunes

I posted this on the iTunes forum, but no answer came back. I wonder if any audio pros out there might be able to cast some light on this:
My computer outputs through a MOTU pci card to an array of Motu2408s and DA/AD converters into a 40 channel desk.
All is fine, except iTunes. When playing audio or video from iTunes i get a gradual build up of crackling noise. It sounds like static discharge. It will build until the music or film track is inaudible. If I stop play it will gradually reduce to nothing, but will gradually build again when I start playing.
This doesn't happen in Logic Pro, Final Cut Pro, Soundtrack Pro, DVD player, QuickTime Player, nor playing the same audio/video files in a finder windows.
Any ideas?
Thanks everyone
Peter
Further to the iTunes post:
I find my son has the same problem, though not so seriously on his macbook pro/M-Audio Firewire Solo combination. Again only with iTunes, not with Logic (Express).
All volume sliders (iTunes, DVD player and System) are set between 40 and 60%,

My initial reaction is that it's a clocking issue. I have had a similar experience when trying to play something in iTunes whilst Logic was open. In my case my Fireface 800 was externally clocked from a S/PDIF source at that seemedto be the reason why. Once I changed to internal clock, iTunes played corectly.

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