I don't follow what you mean by "from 3KHz to 0Hz" pulse. If your frequency is steady and your pulses are connected to the Input #3, then PULSEFREQUENCY(1) should return a value equivalent to the frequency of the incoming pulses provide the electrical spec of the pulses matches the ON/OFF voltage requirement of the PLC.
Can you describe what is the frequency value obtained vs the actual frequency of the wave form? What is the peak to peak voltage of the incoming pulses and is the pulse generator supplying negative voltage with respect to the PLC's 0V power supply?