What size of guide rails did you use?
What type of lead screws did you use (metric/inch)
What units are you using? (you answered that already = mm)
What CAM tool are you using? ie post processing of CAD into GCODE
What are you using for the spindle motor? (how heavy is it?)

Can you post photo of the machine? Showing the x-z axis mount in particular.

My hunch is that there is a lot of movement in the tool in the Y plane. This is due to over large tolerances in the bearing blocks (I have the same problem after 18 months) and the X-axis rail mounts. The MDF bearing blocks compress with vibration and lubricating oil thus allowing for a very large movement in the tool typ. 5mm

So to prove the hunch ... park the spindle in the middle of the X plane. Put the tool into the spindle motor. Drive the tool down to just above the table. Turn EVERY thing OFF. (or risk loosing fingers). Pull on the tool and see what movement there is and what force is needed to move it. Look for flexing in the guide rails, movement in the bearing blocks, look for sleeves falling out of their mounts (oh yes!).

Templecorran
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where the light was kept in the Dark Ages