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yes, you can get interference between the wiring for the fan and the thermocouple wires, particularly when the fan wires are being pulsed to produce slower speeds.
Try to keep the wires for the fan as far away from the wires that go from the thermocouple to the little amplifier board on top of the print head, and see if that helps.
See also this current thread, which is basically about the same thing (but to the point where it actually causes the printer to freak out and shut off because it thinks things are getting too hot):
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illuminarti 18
yes, you can get interference between the wiring for the fan and the thermocouple wires, particularly when the fan wires are being pulsed to produce slower speeds.
Try to keep the wires for the fan as far away from the wires that go from the thermocouple to the little amplifier board on top of the print head, and see if that helps.
See also this current thread, which is basically about the same thing (but to the point where it actually causes the printer to freak out and shut off because it thinks things are getting too hot):
http://umforum.ultimaker.com/index.php?/topic/5254-ultimaker-1-maxtemp-triggered-by-cooling-fan/
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