Wires, or too much clipping on the amp, drop in voltage to the amp as its drawing too much, could be a host of things. But my money would be on wiring not up for the job. Make sure you have a good earth and good live. Then if that doesnt stop it, look to the head unit, it maybe pushing its limits with the subwoofer.
Are you powering it thou a RCA from the head unit, or from the rear speaker signals to RCA conversion?