It's possible that ground based noise is causing problems with USB. What this means is your controller might be earthed via usb through your laptop & then it's connected to your pa & grounded through the amp/speakers. If there's a ground loop you can end up with noise (which you might not even be able to hear) that's mucking up usb communications sometimes.

Try running the laptop on battery & see if it stops the problem. If it does, maybe using a usb isolator will help. Mind then, so might disconnecting the ground wires in the xlrs at the speaker/amp end. Nb this is safe to do & IS NOT akin to disconnecting the mains earth from your laptop, controller or PA!