You would think the processing is after the digital. Call Wadia (734)786-9611 to find out for sure. I will try mine later to find out because I use the "Rock" EQ setting on my iPhone.
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Holy Crap! You're right - I just went in and checked mine, and EQ adjustments on my iPod Classic 120GB *ARE* heard through my system. I've gloated to myself how a CD in my transport going through my CAL Alpha DAC doesn't sound as good as the same CD downloaded in Apple Lossless format into iTunes and then played from the Wadia through the same DAC. I thought I had eliminited all the variables when I did my comparisons.
This changes all that (I, too, use the 'Rock' EQ setting on my iPod when listening via my earbuds), and seems totally counterintuitive that the iPod's EQ settings would affect the 'purely' *digital* output. What's weird is I could swear that when I've used a regular docking station (like I have in my car) changes in EQ settings aren't heard then - I've previously only heard differences in EQ settings when using the headphone 'out' on the iPod.
I just checked mine and you guys are right that the sound changes and I am using coax out of the Wadia into a PS Audio DL III. I don't get it but maybe the EQ is imposed in the digital stage prior to output. My new Alpine car stereo does the same thing but I didn't expect that to be the same as the Wadia transport. Still sounds good but that's because of the DAC IMHO.