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My peek fan works as it should, "virtually connected to the hot end power". My layer fan runs intermittently when I manually turn it on while the print is running. Shouldn't it run as long as I have the button clicked? It does when a print isn't running. Is there a gcode that is defaulting it to off? Thanks for any help.

The layer fan is typically controlled by the code that's generated by the slicing software. If it's sending a speed command to the layer fan channel, then that'll override whatever you've set in Repetier Host.

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