Since I got my Duet Maestro a few weeks ago I had been struggling with setup of motors and extrusion.
I was able to print simple square/straight objects fine some curved objects and infill could sometimes be largely under extruded in places.
Just last night I had finally realised what was happening. I had not realised until yesterday that previously with Marlin I had used absolute extrusion and Reprap defaults to relative extrusion, Cura had correctly switched to relative so the gcode was fine.
What I think was happening is that with relative, there were lines of gcode with extremely small extrudes due to tight curves, if they were smaller than the threshold of one microstep no extrusion would occur. So even if within a curve there would be a large amount of these small extrudes none would actually happen as they are all under the amount of one step. On absolute extrusion I expect that even if it misses a few extrudes due to being too small it will catch up when the absolute value reaches the threshold.
Once i had realised what was going on, the solution seems simple, up the microsteps. I was on 16 Interpolated and went straight to 256 microsteps instead. I printed something that was failing constantly and the under extrusion was gone.
Apologies if this is extremely obvious but it took me a lot of failing and head scratching to work this out. The solution seems perfectly logical but it makes me wonder whether the firmware should really build up extrusions that are too small until they can be handled with your steps per mm (I suppose if this was the case you may as well be using absolute extrusion).