Hmm, after re-reading your post I see that the problem is those last two (high) lines in the song that don't go through. A number of questions: Are you using the headphones jack on the iPod or a line out (say, from the dock)? If it's headphones, what is the volume level on the iPod and the gain set at on the board? How is the iPod connected to the board,
XLR or 1/4"? Have you tried connecting the iPod directly to the powered Peavey board to see if it's problem with the Spirit 8?
Edit: Have you tried burning the song to CD and running it off of that? what is the result?