You've sort of answered your own question here. What are your music files sampled at?
Music dose not have nearly the same amount of dynamic that movies have these days 80% of music rolls off at around 30Hz and once you compress the files into an mp3 file particularly anything less then 160kbs you will loose allot.
How are you getting the sound from the ipod to the speakers, through a receiver. Do you play it in a Pure direct mode? as this will shut off the sub completely in most receivers.