Check the power and ground connections.
As it's getting hot due to excess current running though something aka a short which causes the MCU to shutdown.
Is the Arduino 16 pin chip getting hot? Is that what you meant?
This there anything on the smart controller that is shorting a positive connection, maybe dust causing high resistance ?
Does the fault occur when the hot end is on or the bed is heating and printer is not printing?
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Printer: Ormerod 2 (528.4) Duel extruder set-up with Aluminium X-Rib, RRPro Firmware v1.11-ch (2016-04-08)