Y axis stutters during movement

So I am buildilng self-sourced vc4 500. During commisioning at bed mesh scan I noticed that Y axis moves slighy up and down. Also when I do slight movement from Mainsail just on Y direction, it starts with quite high vibration, that doesnt happened on X axis movement. I got mesh at 0.183 on a cold and very low gantry twist report. By hand all movements feel smooth.

What I did:

Checked pulleys;
Swapped stepper drivers;
Checked motors resistance - all windings equal;
X-Y joiners hit metal back plate equally at the same time;
Switched to standard mode from Performance, feels smoother but the issues still persist with moving Y up and down during bed mesh scan.

Please check video, it is hard to see the vibrations but it is there.

Any thoughts what it could be?