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ronnyking --
Yep, the fan tach is connected directly to the arduino pin. I've had that same issue at times, for me it was incorrect wiring... I had a flipped +12v and PWM signal once, had the PWM flipped with the TACH another time.
I'd suggest getting out a multimeter and testing each of the four pins as you go from 0% to 50% to 100% on the fans. That was the cleanest way of identifying which pin was which -- if you have the ground pin connected to the multimeter ground, you should see 0V across the +12v pin at 0% speed and 12v at both 50% and 100% speed... whereas the voltage across the PWM pin should increase as you ramp up fan speed.
I can commiserate though, for whatever reason the fan circuits and wiring have given me a lot of trouble, often because a pin gets swapped somewhere and then I have to trace it back to where I went wrong.
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