Iphone 4s Sound

To be honest, im not sure if this is an iPhone or iTunes issue but ever since i have upgraded iTunes and/or gotten the 4S, I have been experiencing sound quality issues with only some of the songs while playing the iPhone through my car stereo(Pioneer 3200UB) via the ipod cable. I have used multiple ipods, an iTouch and an Android os based phone and all of them sound perfectly fine. Would anyone know how to fix this issue? thanks.