When you are creating a footprint in your favorite CAD program, or reusing someone else's footprint, double check the zero orientation. This post discusses the IPC-7351 specified zero rotation orientation.
This picture on the left shows a library component with the improper zero rotation orientation. Your centroid file will never be correct if you start from the wrong point.
IPC-7351 states that the LED should be oriented horizontally and the cathode (pin 1) should be to the left. Obviously, vertical and cathode up is not the same thing as horizontal and cathode left. If it's obvious, why do I feel the need to state it? I don't know. I just do.
Red is gray and Yellow white
But IPC decides which is right