Recently my PC has been acting up while I'm playing with a wired xbox 360 controller. After a few minutes playing FPS drops dramatically while I'm using the controller, but when I move the mouse it goes back to normal. I tried playing with the power options, device manager power management, scanning for malware and nothing. It happens when I watch videos too. Any input will be much appreciated.
The fact that the controller is causing harm confuses me. Are you playing on a laptop or netbook? If its battery is dying then there might not be enough power comming from your USB output.
How long has it been since you formatted your hard drive and reinstalled a clean version of your OS (both Windows and Mac's need this done at least once a year)?
You sure you do not have malware? What did you use? I try TDSSkiller, then both Malwarebytes and Kaspersky Virus Removal Tool because no one app is effective enough. This problem sounds more like a virus problem than anything else.
Try going into your devices tab and delete your driver for the controller, then restart your OS and let the driver install again.