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Cant separate click from music on Ipod

My band uses sequences. We have them on an Ipod and send the click (left channel) to one channel on the mixer and music (right) to another channel. Obviously the music is the only thing that comes out the mains, the click go to our ears.
The guy in the band who put all the music on the Ipod and plugs it into the mixer is no longer with us and I cant seem to figure out why I cant get it to work.
First of all, the sequences are recorded correctly, panned for what we desire. Im using a 1/8 stereo plug out of the Ipod and splitting it into 2 mono 1/4 plugs that go into seperate mixer channels.
After using Itunes to load them into the ipod, both the music and click come out of both mixer channels.
I tried the same cable setup and streamed them off of our Dropbox account and it works fine.
This makes me think that there is a setting in Itunes that Im missing. Can anyone help?