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Originally Posted by Kevin Sevcik
The voltage shouldn't be a simple square wave if there's motor in the system. DC motors generate back EMF and also present a fairly large inductance to the speed controller. All of this will have a definite effect on the voltage that you see on the scope with a motor connected.
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You're right, I was thinking about the motor at stall and forgot about the back EMF. The cleanest PWM signal will be with no motor attached.