steppers are rated 20A max, consequently, switching 10-20A into an 
inductive load creates quite a bit of noise.
 >
 > The problem I am seeing is not uncommon for chopped steppers, ie that 
the chopper settles on a subharmonic of the switching frequency (20kHz) 
because of crosstalk.
 >
 > I have tried moving stuff around on the prototype board and looking 
at various grounding strategies. I have separated AGND and DGND in the 
schematic and then joined them, but that makes KICAD treat them together 
as a net. What should I do? Put in a 0 ohm resistor where I join them to 
keep filled zones separate?

In the absence of somebody that really knows what they are talking 
about, I will try and help.  I recently had problems like this with a 
switching power supply.  I built a 1 inch diameter, circular wire loop 
across the two leads of my oscilloscope.  Then I hovered the loop over 
the board and used it as a noise detector.  I found distinct sources of 
noise and these would sharply fall off if you moved the loop away from them.

Then the game becomes to put distance between those sources and anything 
that cannot tolerate noise.  You can use ground islands which have 
isthmuses to connect them together.  But I would never forget that it 
usually takes a current loop to generate noise, and the size of that 
loop determines the amplitude of the noise.  The problem with chopping 
up your ground plane can be that you extend the size of the loop.  You 
always want to get the "return path" (i.e. ground, or ground plane), 
directly under the "source path" so that the loop is only the thickness 
of your board layer, and the orientation of that loop is generating 
noise parallel to the board, not perpendicular to it.  Think of the loop 
as being partially on one layer, and partially on a layer DIRECTLY 
underneath it.

Hope this helps.  A few more prototypes may lead you to answer.

Dick

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