On my machine with the v6 tools I don't have control over any of the part cooling fans, it's either at 100% or it they remain stationary and just emitt a buzzing sound instead of flowing air. I measured the output with a multimeter, the pwm control from the duet seems fine. Anyone else had an issues with these fans? One of mine was dead out of the box, I replaced it with a same form-factor fan, and that gave me speed control over that tool. (can't use the replacement fan though, the airflow even at max is pathetic.)
For toolhead zero you can add F25000 to the fan definition in config.g to get it to work. I don't know of a workaround for the other fans as of yet as the duex does not have adjustable PWM frequencies.