That was quite the shitty answer, especially from the mod.
I fixed this problem by adjusting the volume on the speakers themselves down to about 15%. Than I used the pc's volume to control volume from then on.
Think of the volume knob on the speaker as the gain setting on an amplifier, because I'm pretty sure that is literally what it is. I've seen the same issue of annoying buzz in my car's speaker system, solved by adjusting the gain.
The reason gain is important is because the ports on your pc send the audio signal out at a certain voltage magnitude and gain matches the output of your amp(in the sub) to the input from your PC. If you don't do this it can result in clipping and white noise.
Might even swap out the amp inside the sub if I ever feel like taking on another diy, because the speakers are not being used to their full capability.
edit: When setting the gain on the speakers, set your pc volume to full and play music. This way you know the speakers will output at their maximum possible decibels without the annoying noise.