After some more joint investigation with the test version of the motion interface we found that the problem seems to be caused by a commanding with a too high velocity that was then limited by the set motion limits and resulted in a too low speed. So the axes couldn't quite following the commands.
EDIT: I also want to add the note, that this application can/will lead to strange movement. The motion command always plan with an end velocity of 0 mm/s (full stop at the target position). This means, when a motion with a length of 15 µm is commanded and the acceleration is 25 mm/s², it will only get to a velocity of ~0,875 mm/s. When you have a higher initial velocity (because its a non-buffered command), this will lead to an overshoot. This means, the ctrlX MOTION breaks with the allowed limit deceleration, changes the direction and moves back to the target position.
Currently, there is no way implemented to command cyclic set points to the ctrlX MOTION.
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