some cds are pre programmed with extra bass which, when you add more by using an EQ distortes the sound, this happens even on hifi's. all you need to do is note which songs are doing this, and change the EQ for those songs in itunes to flat or off and then update your ipod. then you can have your ipod set to any EQ but when it gets to these songs, it will play them at flat, and as they already have all that extra bass, will still sound great.
I hope this helps