Are you using the mini jack on the ipod or the plug on the bottom. I've read that the onboard amp is not so good, but you can bypass it and have cleaner sound, if you pair it with a Line out cable to something like this......
http://www.headphone.com/headphone-amps/headroom-balanced-ultra-desktop-amp.php
or one of their desktop stereo amps.
but then, it gets a lot less portable, so whats the point.
Anyway I'm sure it will all sound the same coming out of any non hifi boombox including the mighty M90.