PWM pulses line up better with this waveform then with the input because there is less of a delay.There still is some delay that is associated with phase delays in the low pass filter.The output waveform is also very choppy.This behavior is due the fact that the PWM frequency is so low that some of it still ends of in the output of the low pass filter.If you were to zoom in you could see faint remnants of the 8000Hz PWM pulses.The figure shown above is the input waveform from the function generator above, and the output waveform of the PWM passed through the low pass filter.