My Brera 10cd changer Blaunpunkt in the boot has exactly the same problem, and it's even worse with the burnt CD's than it is with Studio CD's. I know some car CD changers have an "Orientation mode" on them (usually hidden when the CD cassette goes in) for horizontal or vertical playback but I can't find one on this unit.
Do you use Aux, an FM transmitter or USB for iPod? Apple have a very poor DAC inside the iPod's and you actually get better sound by using the USB on the bottom. Also make sure "Sound Check" and "EQ" is OFF.
Check what quality your music is. "Ripped" audio from Youtube will ALWAYS sound worse, as you never know what bitrate the original source file was. Because I'm mega fussy when it comes to sound quality I compare the same song released on different albums using spotify and then purchase that on iTunes or Amazon. Sometimes remastered sounds better, sometimes worse.