I don't know what happened??

[tbendtom]

I have a 2010 yaris; today I left the ignition key on and the battery almost drained. There was still enough left that the presets on the radio and the clock was still correct. I used my boat bat. to jump start the car...Now I find that my ipod will not come on in the aux position (it did in the aux position before I let the battery go down). My car has a aux pig-tail in the glove box that plugs in to the ipod. Cds still work, I can plug a music player in to the aux jack by the break lever and it works through the aux. I seems that if the radio is on I can't get the ipod to work...But, when I disconnect the ipod and reconnect it, it will play until I switch back to the radio, then attempt to reconnect to the ipod it will not work, the aux button brings no results; nothing on the display either...What am I doing wrong?