Driving the iPod to 95% could plausibly be causing an audible amount of distortion.
Given that the HE-500 is a relatively low impedance headphone, we're pushing heavy on the current. It's possible that the headphone amp inside of the iPod is struggling to put out the current required for 95% volume and is introducing distortion. This added distortion would reduce the imaging on the HE-500 and reduce potential soundstage wideness or detailing.
One test that I would try is to use the iPod at a lower volume and do your best to level match with your amp, then compare to see if you can tell a difference with the sound.