So switching to PID did solve the problem.
You don't have to read the rest.
I am curious why this happens. On the SeeMeCnc forum one person attributed it to the hot end temperature changing, but my hot end temperature was steady. This is why I assumed there was a changing speed on the extruder.
I am also using a Bondtech extruder, so I wonder if it is more noticeable on a geared extruder.
Does it only happen when you run an SSR or Mosfet? Using these the current on the Duet for the bed heater is very small. Does it happen when running the heater through the Duet?
Anyway, I am finally getting decent prints (I introduced and fixed several issues when converting a Rostock V2 to V3)
I am loving the Duet Wifi.