Make sure that your comparison is done at equal volumes. In an A-B comparison, the human ear often perceives the louder signal as having better quality. (There is valid physiological reason for this, since at lower volume the ear is less sensitive to both high and low frequencies.) Since iTunes tends to run a little "muffled" compared to other players, you may have to turn it up to get a fair comparison.
Feel free to report back with your results, one way or the other.