I think I know what you mean, could you send me a video to philippe.habets@vectioneer.com.
Does this happen each time at the same frequency, regardless of the speed. So for slow motion and fast motion the ticking frequency is the same.
1) What you can do, check if the signal send to the drive is smooth, https://desk.motorcortex.io/, path: root/Ethercat/Robot/Axis1/In/Target position
. Don't forget to set the update rate to 1khz (Settings). https://docs.motorcortex.io/docs/motorcortex-io-tools/motorcortex-desk/#screen-lay-out
2) You are sending to root/Control/jointManualPositions
this is incorrect.
You have to stream your positions to jointAutoSetpointGenerator/input
set fade time to 0 jointAutoSetpointGenerator/fadetime = 0
root/Control/gotoPauseMode = 0
root/Control/gotoManualMode = 0
root/Control/gotoMotionplayerMode = 0
These should be the settings to stream position with the generic app
3) If you run the motor though code, you should not forget to reference, else these jumps will occure.