Ok, I've run the printer with the board out, it seems the cause of the heat seems to be an adjacent connector starting to melt! This one drives the heated print bed. It seems the extra cooling is causing the print bed heater to work much harder in order to keep it at target temperature. I've taken the connector sockets off the board and soldered the wires for the heater directly onto the board. After running a small print, there appears to be no overheating and it works fine.
It does seem that these boards are not capable of adjusting the fan speed, the gcode to run them works with an M106 S0 switching it off and other values 1-255 just power it on a full speed.
Thanks for the help, much appreciated. My fault finding skills need work!