I just installed this system yesterday and had exactly the same problem. I called Crutchfield tech support up and had an answer in 5 minutes.
If you're using your iphone cable into the USB, you have to set the input to AV-in. But it's grayed out.
Go to the main screen and select AV-Off (then you will have access to the AV-in control)
Then go to settings, input, and select av-in
Then plug in your iphone and go to the main screen and select AV-in
From there, everything seems to work.. I can use the ipod and the pandora functions from the screen.
He said there is a JVC proprietary connector (not compatible with Iphone 5) that you would set the input to ipod to use. Gives you a few more functions.
Sometimes crutchfield.com is a few dollars more expensive, but this is why I've bought from them for years. Saved me a ton of time and headache setting up systems.
Les