Official comment
Fixed it. It wasn't the usb port that was the issue it was the Microsoft Mouse and Keyboard detection driver (Wireless dongle for my keyboard)
It worked the last time because i'd removed it to replace it with the RX usb. As soon as I put it back in, that's when it stopped.
I've tested it several times since and Rekordbox works perfectly with the RX when I've the Microsoft wireless dongle removed. I tried to moving it to a port on the back of the machine, incase it was interference from the wireless device, but as soon as the driver installs it will freeze Rekordbox again.
So it's definately the driver for the wireless keyboard that's causing the problem. Guess I need a new keyboard.
This may be helpful for anyone else who experiences similar device breaking latency problems.Remove all usb connected devices and see if it works, if it does try adding each device one by one until you find the problematic device that's causing it.