As the setup part of the sketch functions silently now, I deduce that I do not have a hardware issue.
Below is a video that shows the system running with the above sketch.https://eshare.yr.com/fl/WRZwF9dpUW
I found this article about the pwm and arduino
It mentions that the interrupts can be a source of jitter and that they should be turned off. The 2 & 3 pins that read the CHANNEL A&B data are interrupts and maybe interfering with the map. Is this plausable?
I tried Smoothing the potentiometer
but it has not had any particular effect.