The position of the mid-rail is controlled by line 69 of your KCD Shop Standards. If you go to Change > Set Shop Standards, and scroll down to line 69, you will see that line 69 states "Adjust Reveal Center", and that it is set to 8mm (.315").
We do this to offset (push the mid-rail down) so all but the reveal (typically 3mm or 1/8") is available for doors below to land on, making the bumper pad position on the doors below less critical.
This offset looks something like this (the left image is with line 69 set to 8mm, the right image is with line 69 set to 0mm):
If you prefer this mid-rail be centered as shown in the image to the right, then simply set line 69 to 0mm (0"), and it will stay that way until you change it (KCD updates will not affect settings you change).