6090 Jinan Jidiao CNC - Y Axis problems

Hi, we purchased a 6090 CNC and been using it for a about a year or so without issues, usually for engraving.
Suddenly 1 every 4 engravings or so, it starts to "step up" on its Y axis for lack of better wording, and its messing the whole piece.

Example: if its engraving a figure it will star normally and some place along the middle of the engraving process it would go up on the y axis and start engraving about 5-10 cm up, so one part of the engraving is ok, and the rest is done on the wrong area.

What we been done so far:

It came with a Autorich A11 controller which we already reseted and upgrade the software. (more than once)
Changed the USB used to send the gcode files to the controller. (works fine on our other cnc machine)
We have two controllers so we exchange it for the other, including the controller part inside the machine.
changed the Y and X moto controllers to see if it was a faulty motor controller.
Inspected the long screw that moves the Y axis and it turns smoothly, no rough areas.
We also checked the stepper motor just in case and it runs beautifully.
Verified the y axis limiter and changed it

We don´t think its a mechanical problem because if it was it, the problem should been seen in every engraving done with the machine, instead i 1 out of 4.

We don't know what else could be wrong with the machine, so any help is appreciated.