I'm sorry, but this is absolutely impossible. Lyrics, without a band compressor/limiter, cannot be removed from a stereo mix. without resulting in horrible quality. I highly doubt you have your ipod chained through a limiter, so thats the end of that.
As far as EQ, EQ only boosts or cuts frequencies in a mix... it does not affect the mix. Furthermore, the iPod has NO capability to adjust a mix anyway. This has to be from the source file or hardware issue.
The only thing I can think of is that a contact is crossed causing phase problems. The only thing (usually) perfectly stereo in a mix is vocals, and if phase is flipped 180 degrees, then the vocals will cancel out and be very hard to hear.
It's a contact problem (hardware) within the ipod, or the headphones are wack.