I have a MacPro (desktop model) and I have recently been also getting audio distortion for about a month. I am using Logic Pro with a Mackie Onyx Satellite, Motu Midi Express 128, Mackie Mixer, PC88 keyboard, Alesis PowerAmp. Everything has been fine up until over a month ago when I started to get distortion in everything: Itunes, Keyboard output, Finale (music editing software),LogicPro output. I troubleshot the speakers, power amp, etc. I called Apple Support and they suggested I take the cpu into an Apple Store. I did that and they ran some diagnostics but it showed no problem. I talked to several vendor's tech support concerning their equipment and one felt that it was a communication problem between the firewire of the cpu and audio interface (Mackie Onyx). I purchased another firewire card..... still the same distortion. The next thing to 'change' is the audio interface.
Occasionaly when I re-boot, the distortion goes away and if I use Itunes or play the keyboard all is well..... until I use Logic Pro or Finale. I am starting to believe that it is software related and that some software is changing a setting causing the distortion.