You could try making on of these test probes. Attach the clip to the ground tab on the jack, plug the guitar into your amp and then progressively touch the bare wire on parts of the circuit. Whatever is playing on the iPod should come through your amp. As you work backwards through the circuit will get to the pace where you start to have the problems and you should be able to isolate where the issue is.
(It's worked so far for me anyway.)