Scara kinematics

Is the problem at the point where the elbow inverts?
Many positions with SCARA can be reached in two ways, and the kins has to avoid flipping between them.

No. This is inside the rectangular area that can be reached without inverting. As far as I can tell, there's nothing special about it..

Can you try capturing the joint position commands with Halscope when the problem occurs?

Sure but I might need a bit more guidance setting this up. My halscope kung-fu is pretty weak.

Do you mean the a-pos-cmd on the signals tab in halscope? Not sure what that corresponds to as I have joints 0,1,2,3 joint mode and axes XYZ in world mode.

A screenshot or guide how to set up halscope to capture this kind of error would be very helpful.

I think that the interesting pins are the three joint.N.motor-pos-cmd pins.

If those jump by more than a f-error then that's the problem.

Also log the motor-pos-fb pins. Perhaps this is an encoder reset?

I'm not sure how to interpret this. Does it make sense?
imgur.com/t2aejTN

BTW, I have run both Machinekit and Linuxcnc on this machine. At the moment, I'm set up for machinekit because I'm testing a remote UI being developed to embed in FreeCAD. If you think that's related, I can reinstall with linuxcnc. Any issues building with Debian Buster?