Hi Stephane,
Perhaps some more details of your machine and it’s set-up may be helpful in identifying the problem.
If you have an occasional ‘tick’ when driving your stepper motors from one end to the other end of an axis travel then this could indicate ‘lost steps’. If any of your stepper motors make this occasional ‘tick’ when stationary then I would suspect the problem is electrical noise.
Is your limit switches and e-stop wiring made with shielded cable ??
Also….If you return to the main forum page then carry out a search for ‘lost steps’ you will find many suggestions, some of which may be helpful to resolving your problem.
Tweakie.