Lee,
sorry to hear that you're also suffering the dreaded Alternator Whine, but I can assure you that I don't get the whine on mine, even when belting along the motorway at .. ummm .. 70mph (Officer) with the music on ... err ... loud /ubbthreads/images/graemlins/groovy.gif
As Andy has suggested, it's a good idea to check all the cables and make sure that there is good electical contact.
The other threads on the PhatNoise forum are related to VW Jettas, but there are a number of people with other VAG cars that don't have a problem /ubbthreads/images/graemlins/confused.gif
I have a new-style Audi Phatbox that doesn't have the RCA Stereo Out Connectors - the audio is passed back up the Audi CD Changer Cable from the "centronics" interface at the rear of the unit.
Fitted the CD Changer cable myself - had to order one in from VAGParts.com as I didn't get one with my car (cheapskate Audi) - so I took care to route the cable behind the GloveBox, via the LHS Door Sill, behind the LHS rear cabin interior trim and into the boot. Same job as when I ran the Control and Audio Cables to/from the boot for my old Sony MiniDisc Changer - never had any alternator whine on that either...
Perhaps the folks at PhatNoise have fixed the Alternator Whine issue with the new design PhatBox? Could Audi have improved the quality of their CD Changer Cables? /ubbthreads/images/graemlins/shocked.gif
FYI, my car is an MY01 S3, built sometime in the week begining 5th July 2001. It has heated electric Recaro Sports Seats, electric sunroof, heated door-mirrors (shiny ones), auto-dip rear-view mirror, BOSE Speaker System, Audi Concert (v1) Radio/Cassette, Cruise Control, DBW Throttle, Electric Door Windows and a 210BHP ECU. Which results in a heck of a lot of electronics all being fed through the dashboard area.
Maybe I got "lucky" with the wiring on my S3, I'll be sure to flag that as a feature when I come to trade it in /ubbthreads/images/graemlins/wink.gif
Mark.
P.S. I do get a very loud buzzing/humming sound on MW Radio from time to time which I've tried to isolate, but without success /ubbthreads/images/graemlins/frown.gif