Ethercat random jitter fix

Another thing that comes to mind, do your servos have braking feature? The clunking and the resonance could be related to that if you do have brakes, possibly they are not being properly managed? I use braking on my Z servo drive, and if I lock it when idle I have resonance as well, that's the only thing that comes to mind, also it does make a noise when it engages more of a click than a clunk, just my brain went there...