No the wires are fine.
I've just wired it as a normal 12v psu and put the jumper for 5v back to int.
Everything works fine. The motors, heaters, fans etc. Looks like the problem is with the Ext 5v/PS on connector.
From this I looked at the schematics and the PS on circuit goes through TR7.
It took some finding as it is tiny but I have found it and it is burnt out.
I have another Duet Wifi that doesn't use PS on so I can swap them over.
Thanks for your help with this.