Yesterday evening, I measured the stabilization accuracy of the scanhead. I repeated the following;
enable the scanhead, stabilize it (get it in sync) sent out pixel 3600 and record the image with an exposure time of 50 ms.
The result; spot is extremely stable. I measure a standard deviation over 21 measurements in the x- and y-direction of [0, 2.2]  micron.  Note that this is expected as the y-axis of the camera was parallel to the scanning direction.  I have added the measurements as rar file, see 21measurements.rar.

Summarizing; repeatability in scanning direction after disable/enable scanhead is 2.2 micron.