Last I looked, AMP is just using Quicktime to play the audio which is what I believe iTunes does as well actually (but could be wrong).
One thing iTunes offers that AMP doesn't is an EQ. It could be that you have either the global or local (per song) EQ turned on. If so, turn it off and see if that helps.
I personally have never noticed a difference between AMP and iTunes as far as SQ, but I run directly to my Amps rather to a head-unit so I wouldn't run into conflicting EQ setting issues.