Some good news! (sorry if I don't use the right technical terms).
More information about the printer that electrical members mentioned:
the motor cables are long (more than 2m for Y and more than 1m for X) and not shielded (we changed this at the end). the X and Y motors are bigger than needed (we are moving them with 2.5A but they are least 6A). the 24V cable to the Board 3 6HC is 1m and I belive there are 5m to the scanner.Yesterday, we removed the ferrites and measured with a probe the 24V line. Just turning on Y motor was enough to see how the noise increased a lot. As the motor cables and the 24V cables travel next to each other in the printer, they believe there is interferance. The next step was to change the motor cables for shielded ones and it improved the results.
Today, the line filters arrived and after installing them, the problem seams to be solved. One filter is close to the extruder+scanner and one is the Board 3 6HC.