I have an 80GB iPod hooked up through the USB port on my JBL Nav system. It works great, but every time I start the car, I need to unplug and plug the iPod back in for it to recognize it again. It's not a huge deal, but I'm not sure why it loses the iPod when the car gets shut off.
mine used to do that, it does not do it anymore. I have a mdl II 2012, but I have noticed that I think the dealer did some software upgrades over the past year that may have fixed it. I have done nothing myself.