You may want to download
MP3Gain and run some of the offending songs through it. You will probably see that they are clipping, which means that the headphone amp in the iPod will produce distorted sound. Using the EQ only makes the distortion worse.
MP3Gain allows you to reduce the overall gain of tracks, thereby reducing (or eliminating) clipping. The program allows you to analyze the tracks first, then make changes if desired.
I've run MP3Gain and applied the suggested changes to most of my library. I had many songs that sounded awful until I applied the gain reduction. Be sure to read the help file after installing it so that you understand what all of the options are.