Hi Harry,
After somewhat humiliatingly reading this was the number 1 email/post to DDJT, I steeled myself to navigate the labyrinth that is the Virtual DJ forums in search of an answer. I found going in via Google to be a better way and eventually stumbled across this page: http://www.virtualdj.com/wiki/MixTrack%20Pro.html.
I thought I had tried this configuration – obviously not. It now works the way it should.
It did make me wonder though, if this is the number one question, why is it so hard to find a simple answer on DDJT?
Harry, thanks for your response, that is your good deed for the day.