Well I had the DMF replaced, and it was the same. The car is now at VWR and they are removing the box, and If they cannot sort it, they will put the car back to standard and remove the LSD.
VWR have given me a MK6 1.4 TSi and it is a very nice drive, slightly bland, but very comfortable, with a lot of nice touches. They had offered the Red tuning Golf, but I did not want it, had it for a week last time and did not like it, could not face driving a bone-shaker for another week, not my sort of car. I was also recently told it was no better.
So here is hoping, Matt has 100% agreed that there is a problem, not what you would expect on a 2 year 17k old non mapped Ed30. The clunk had been there since the LSD fit.