I get most my "Odd" extrusion problems from heat creep from the throat of the nozzle into the heater block. How is the second extruder cooled compared to the first one? Have you tested to ensure both fans are performing equally (I am assuming dual fans). Is there anything blocking airflow? I once had the ornamental piece for the Hero Me 5 cooling duct cause me all kinds of issues because it restricted airflow to the hotend.