Okay,
I have done some tinkering and think I have found a fix to this. This is plugged into my computers USB and anything connected to my computer directly(headphone jacks,speakers powered by my computers USB) has the terrible hum and noise when the lights on the controller light up.
So trying to use the controller with line in on my computer to use headphones to mix is a total no go unless I want to deal with the background noise. Also I was getting the same issues with my powered speaker because it was also being powered by a cord coming from my computers USB.
So I changed the power cord going to my speakers from one coming from my computers USB to one from the wall outlet and it totally made all the background noise go away. Even with the USB powering my speakers from my computer it still gave the same bad background noise.
Seems like pioneer does not fix these things when designing these products. Shame.
But at least it is working as intended(mostly) now :/