Wrong cut

[m_c]

It's more likely to be spindle deflection.
You say you've measured deflection on each axis, but what about on the spindle nose/cutter with the spindle at cutting depth?

[cncnescu]

I already checked the spindle and has no runout(0.01-0.02) and also no deflection. The cutter is a 4mm x22mm (not the best quality) and for sure will deflect. Tomorrow I will check this too.
However, the cut was done first at 2000mm/min and second at 1000mm/mm and decreasing the feed rate /deep of the cut improve the result, but not dramatically(from 39.7 to 39.8).In case of cutter deflection changing the speed/deep should improve the result.

[magicniner]

I already checked the spindle and has no runout(0.01-0.02) and also no deflection..

Have you investigated the side-force generated by your cuts and applied that force via a bar in the chuck, with the same protrusion as your cutter, to measure deflection?
If not then your measurements are not valid,
Regards,
Nick