I've had this happen about 3-4 times on my 2005 GT. The first time they replaced the radio under warranty, but its well out of warranty now.
What seems to happen is:
- Playing CDs on the radio
- Shut down car with radio on and in CD position
- Radio does not completely shut off when the car is shut off and the door is opened
- The only circuit left active in the radio is related to shuffling the CDs, and it starts randomly shuffling the CDs in the radio (you can hear it if you are paying attention as you get out of the car)
- Battery eventually runs down completely
- When car is jumped and turned back on, the radio displays a CD read error, and appears to not work at all
I can't tell you exactly what I've done to get it back to normal, since I've just played with the radio by switching modes and hitting the CD load button, and it finally went back to normal. I have now removed the CDs from my radio, and I always manually shut the radio off before I turn the car off. This seems to be a good work-around.