Okay, I just did a quickie listening session for you. Basically I hear the same things that you do. I think what you are hearing is a result of the ipod's dac. There are other players that might improve the sound. I do agree that when used alone with the pc, the e17 sounds noticeably better. The easy solution would be to use the hardware EQ of the e17 to get the sound back to where you like it. I'd say that plus 4 on the treble would be a good place to start.
I've also got hopes that a new cable that I've ordered will accomplish some of the things that I think you're after.
I should have it in a few days and will report back.
Hope that this helps...