I was thinking about this and I don't see how the radio can affect it unless it's miswired. I can't think of any reason for an aftermarket radio to be connected to the serial data bus in the car. My guess is it's miswired and something is incorrectly wired to the data bus line.
Someone correct me if I am wrong here. I've driven my 04 GTO without the radio installed and nothing bad happened. Since it doesn't care if the radio is missing, there is no reason for an aftermarket radio to cause problems unless it's miswired.