QTplasmaC wont turn on

I doubt this is the problem, but can you verify auto repeat is off?  It is off by default, but I didn't see the line in your old config anywhere.  Can you verify that in your preferences file (should be TN3.prefs) that the following line exists in the [GUI_OPTIONS] section:

Better yet, with QtPlasmaC running, open a terminal window and type:
Under "Keyboard Control" it will show "auto repeat" and whether or not it is off or on.

I'm assuming you are jogging with the keyboard.  Do the motors only vibrate when jogging with the keyboard?  Can you try GUI jogging and see if they still vibrate?

I'll caveat all of this with the fact that I couldn't discern much in the video, but your video did jog (no pun intended) my memory of the auto repeat stuff from the past.

Also, now that you've updated everything it may be useful for you to post a new backup of your config.
 

Are those step/dir controlled servos?
Sounds like pinions are pressing way to hard on the rack or are misaligned, but knowing you i doubt both.
Check the step dir timings and make those a bit longer
Try running the servos from their own control, so without LinuxCNC just to be sure where to look.
And just in case regarding the first point, check the scaling on both Y joints/axis, same noise would be if those are a bit off.
And check if the pinions are tightened.