Hi Geert,
Thanks for taking the time to look at my case!
Of course, my printer is an Ultimaker (2+ Ext). For a short while, I thought that a ball bearing might be broken but, I think there is no ball bearing on that shaft, only a brass sleeve. I just lubricated the shaft (using the grease supplied with the machine) and slided it many times (with the power turned off). Then I tried another print and got the same vibration.
With the power turned off, I moved the extruder and felt the vibration and hear a noise. I think it comes from the bearing but that's difficult to be sure. Could it be a stepper motor?
We own two identical Ultimakers, of course the second one don't vibrate and make no sound while the extruder is moving toward the y axis.
I'll make another print attempt placing the cube somewhere else on the bed to determine if the same vibration will occur...
Best regards