Make sure to turn off the "sound check" and "sound enhancer" settings. Also make sure the EQ is turned off.
Another issue in mobile audio is the output. To really get the best out of an iPod, you must use a dock that allows the digital signal to be the output, not the analog, which uses the internal DAC chip. Using a dock that allows the digital signal to be processed by an external DAC can make the iPod sound better than most consumer CD players. When done right, it sounds extremely good.
There are a few docks that allow this in a home system such as the Wadia and Onkyo. I also have a DAC that allows a direct digital connection with an iPod. As for such an item for mobile applications, I'm not sure what is available.
Hope this helps....