On the control pod, i have a cord that has three 3.5mm ends plugged into 3 ports labeled "6 channel direct". That cord goes from my control pod to my computer and plugs into the 3.5mm headphone jack on my computer. So i believe the answer would be 6 channel direct?
I think that might be the issue, but let's walk through this.
First, you'll want to have the selector switch on the back of the control pod set to "Stereo 1-3" instead of "6 Ch. Direct." The 6 channel direct setting is for when you are using a 5.1 sound card, for which one of the jacks is for the front left/right speaker signals, one jack is for the rear left/right speaker signals, and the last jack is for the center/sub speaker signals. Because you are only sending a stereo signal to the unit, select the "Stereo 1-3" position. That position will treat all three of those inputs as individual stereo inputs, and you only need to connect your computer to one of them.
If your speakers didn't come with the manuals, you can download them directly from Logitech. Here are the links for the
Installation Guide and the
Setup Installation Guide.
The setup manual will help explain some of the different audio choices in the control pod menu.
Btw, does your computer have a digital audio output (either coax or optical)? If so, that would be a great choice for the connection and would be better than using the headphone jack.