Try disconnecting the power to the stepper drivers and do some spot tests again. Stepper noise could be getting mucking up the PWM signal decoding.
If the graph is different, then PWM filtering is not working very good.
Welcome to the world of Syil spindle control.
My Syil SX3 is not much different to what you have found.


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). The solution was to calibrate the spindle in Mach3. However, that required extra circuitry to provide feedback to Mach3.
I did not look into it further.