Help with Stereo please!!

I have the Clarion XMD3 CD Player and I am having a few issues. This model has 2 AUX inputs and 1 pre0sub out. I plugged my iPod to the one of the inputs and it is only playing through the 2 front speakers (I have 4 total speakers). I played with the balance and fade and switched around the input plugs and nothing. Then, if I change it to the radio, I can still hear the iPod playing along with the radio. What’s going on???

It sounds to me that the XMD3 is not working properly. If that is not the case, make sure you have it plugged in to the same imput and haven not crossed any up. I have the same radio and I thought that it only has one aux and the other are sub and amp outputs, but I could be wrong. The reason I think this is that one is grey, one is black and one is red, like I said, If I remember correctly....

Yeah, I tried every combination with those two inputs and nothing. I can even unplug the red and only have the white plugged in and it will work, but the sound is cut in half.

I am wondering if there is a setting somewhere I am missing.