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In StandardFirmata.ino, systemResetCallback() sets the default mode to OUTPUT (and value LOW) for all pins on startup. This will short-circuit the pins which are connected to HIGH logic level by other circuits, causing malfunctioning or serious damage. The Arduino itself defaults all pins to INPUT mode on power up, which physically can not do any damage and is the only safe mode in any hardware situation.
Please follow this and set the pins mode to INPUT in the sketch as well.
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