When there's a channel not working properly, it could be one of four things: a loose connection to the soundcard, the volume control pod wiring, the sub channel, or the soundcard.
Try this test to help determine:
Switch the green and purple plugs in the soundcard. If the problem stays with the speaker plugged into the (which ever channel is out) channel of the sub, then the problem is in the sub or control pod. If the problem moves to a different speaker, then the problem is with the soundcard (you may need to reinstall your drivers—contact soundcard manufacturer for help). If the problem is fixed, then it was a loose connection.