I updated my motherboards 3.0 slots because I bought a 3.0 external hard drive. After doing so I experience crackling/popping with my audiobox usb plugged into a 2.0 port. I have a wired connection, no bluetooth/wireless. 4790k, 16gb ram, 256 ssd. I have a soundblaster sound card I've used in conjunction with my audiobox for more than a year and it doesn't have the same popping and is also a usb device. I've reinstalled the drivers. Tried different ports. The sample rate is 24 bit 4800 and the buffer is at max. I've ran Ccleaner for the registry and I went through the "complete uninstall" for the audiobox. I'm 99% sure it is the usb 3.0 update. I've went through quite a few articles already and nothing has helped.
The only thing I haven't done yet is uninstall the 3.0 update, which I'll do shortly. EDIT - Can confirm this is from the installation of the Intel USB 3.0 eXtensible Host Controller Driver. Works fine with it uninstalled.