I just experienced the same problem- AUX input doesn't respond when pressing CD button. Just hit 51,500 miles.
Last week after returning home, the windows on the driver side refused to close; I quickly realized that all of the switches on both driver side doors (mirror, windows, fuel cap, trunklid, window lockout switch, NONE) stopped working. Passenger side door switches worked fine. Finally I disconnected the battery for 20 minutes and everything returned to normal (***?!?)...
...except that now I have no AUX input. CD, radio, SAT work fine but pressing CD doesn't bring up the AUX input. Sucks, since I use it every day. I doubt the dealer is interested in replacing the radio since the warranty is expired. Any suggestions to reset it?