both use PWM may be ? The Cooler is ok and the fan too. The PWM control change the speed from the fans. If the CPU is cold for example you boot/start the pc the fan will not rotate or it rotate with really low rpm. When the CPU works and the load will be higher, than the fan will rotate with more rpm. Warning can changed in bios. Most times it´s ok if you ignore the fan control (PWM) and when you get the error, than disable the option Configuration Hold on F1 Error. Search it and you will be happy.
I hope this will help you