I may just try that. I know from listening to some of my CDs on my HiFi that some CDs aren't particularly great productions and sound a little flat too. It just seems so much worse in the car (Concert I head unit with Bose). My problem is not so much a lack of treble but a lack of bass and depth to the music. I guess it could be a limitation of the car audio contributing to the problem but I don't remember having this when I was using the CD changer before the Phatbox.
I'll experiment with the tracks that I think sound the worst and see if there is any difference.