A_and_C’s comment about the relay being reliable made me dig deeper. And yes Peter absolutely everything goes through this relay including the starter current so I could do proper testing under load to rule out earthing problems.
I think I found the issue which was probably a loose connection on the coil. I wasn’t sure at first as the relay is jammed down the side of the battery box so you have to take out a load of stuff and swing the relay out. I wasn’t sure if moving the relay for testing caused this connection to become loose or not. Anyway, it has had hours of testing and several flights along with a 2 1/2 hour flight today.
I can confirm there is no diode to soak up the back EMF as if you disconnect the switch wire from the coil and hold on to both connections you get a nice shock, slightly less bad than a cattle fence! I probably took one year off the life of the master switch with all of the arcing during the 100+ switching tests.
I also found some interesting stuff about the resistance of the Master Switch – to be honest it should have a diode added to deal with the back EMF but I suppose that is not technically allowed under the maintenance rules. I am not sure if my master switch resistance testing is too nerdy to post or not!
Nothing is too nerdy 
I would add the diode anyway. Safety always comes first; if you lose electrics while flying you will wish you did it.
