When using the 0.5mm thin wall to calibrate extrusion ratio I discovered, that slic3r 0.9.9-dev seems to make 3 of the 4 walls wider than neccessary by moving the extruder along the x-axis a lot while printing (vibrating along x axis).
figuring this might be related with my 0.4mm nozzle, I created this 0.4mm thin wall (2x2x1cm) and with this, the problem was fixed and I now can calibrate perfectly.