I suggest that you add a ceramic capacitor, 100pF, from the IPOD music input of the transmitter to ground and place it with shortest possible lead length right where the ipod connects to your board. In addition, you might want to try winding the cable that connects the ipod to the transmitter into a coil of about 8 turns with 1 inch diameter (very approximate) with this coiled section being closest to the transmitter, not the ipod.
Both of these things are meant to keep the transmitter RF energy away from the ipod.