you can see in a png screenshot that only a single 3.5 mm hole (upper right one) is a real through hole. All other three ones contain some unexpected plane which partly or completely covers them. This plane is not present in openscad source as well as in openscad-generated stl (viewed by freecad and chitubox). It appears only in .photon file if opened by chitubox or printed on A.P. printer.