Success!
In my case it was a Renesas usb driver for other devices (like mice and keyboards). I use a lot of unique peripherals and this was obviously need to make them work correctly.
Removing this has killed the use of all my chosen USB peripherals and I'm now searching for compatible hardware and drivers that will still allow the arduino to function as well.
I thought this was the whole point of multiple ports - so that you could run different hardware.
What I don't know is if this is an issue with the arduino implementation of the port calls or an overbearing Renesas driver hammering away on all ports, drowning out meek whimpers from the arduinos.