First, and you probably know this, but when you do comparative listens, make sure the volume is equivalent. Otherwise the louder one, even if it is only slightly louder, sounds better.
Second, there are a few settings in iTunes that you can fiddle with and see if it makes a difference. In Edit > Preferences >Playback there is a "Sound Enhancer" that you can adjust. And on a per-song basis, you can go to Get Info > Options and set the Equalizer.
Other than that, what you are hearing is simply the difference in the two players.