Deactivated Freedoms in time domain calculations may not be the most rigorous approach to restricting a structure's motion, due to the way in which the freedom deactivation is applied. The change in position that you see is basically the sum of numerical round-off errors over a large number of time steps. Deactivated Freedoms are usually more appropriate for stability analyses, where we are iterating towards convergence of the forces acting on each structure.
A better approach for this workflow may be to use an arrangement of Fenders between Fixed Points and the pile guide. To restrict motions to Z and RZ only, you will need 8 Fenders on each pile guide, arranged as shown:
Viewed from above:
This approach also allows you to define stiffness and friction terms which may give a more realistic model of the actual pile-jetty connection.
I hope this helps; please let me know if you have any further questions.