Ok Team,
I now have it working.
Rather than copying the Mach3 xml I have followed the BOB setting and input them manually and its Jogging correctly and I tried a small Gcode run and that seems OK. So far so good.
Now I have checked through the settings from the ones I posted earlier and they are exactly the same.
So I am none the wiser as to what has caused the issue in the first place.
Thanks for your comments and I will look at end stops config once I get up in the morning with a fresh head.. Blown it today.
The comment that made me think was "maybe there is a bug in the xml convert tool" from @Robertspark . Thank you very much.
Now going to fill my head up with a glass of scotch to hopefully soothe away the pain.
Thanks again guys, much appreciated.
(I will follow up with the other pins config as well)