Gerd:
Does the cable from the Pioneer to the IPOD connect to the headphone jack on the top of the IPOD, or to the docking connector on the bottom of the IPOD?
If it connects to the headphone jack and you go into IPOD control mode, then the Pioneer most likely ignores the cable input from the headphone jack which is typically connected to an "AUX" input on the Pioneer, not the IPOD control interface. Two different, switchable inputs.
As far as getting out of IPOD Control mode, you'll need to peruse the user manual more closely - there must be something in there to tell you how to toggle in and out of control mode. Usually it's part of the function switch menu - once you get to the IPOD control function, then the left or right arrows usually control toggling a function on or off.
BTW: When I got the radio for my car (a Pioneer, too) I found it complicated enough that I keep the user manual right in the car.
good luck.
gn