To double-check that it is not software related can you plot the setpoint that is going to the drive in our DESK tool:
root/Ethercat/Robot/Axis1/In/Target position
Make sure you set the Frequency Divider to 1, so you see all samples
In DESK, click on Settings and then set the Frequency Divider to 1::

The signal should be smooth, also when you hear the ticking sounds.
Please post your findings here.