So we investigate in the firmware playing a bit with acceleration and jerk, but the results was exactly the same.
Thinking that most of our prints are ok, even when we are printing at high speed, we realize that there is something more in some geometry that generate the problem.
Let's get to the point.
In the firmware, for Sanguinololu for example, the maximum frequency is setted to 15000 Hz.
in reality, even if your motors and electronics can bear such a frequency your mechanical parts probably not.
Think the machine is shaking at very high speed for a very short movement, In that moment the maximum frequency is reached and the steps is getting lost.
We realize that this is happening more often on the Y axis, because of the length of the belt,
In our case it solved the problem and we printed those parts without any further problem