Hi Hugh,
The beam shading factors only reduce the beam (direct normal) component of the solar irradiance incident on the array (in the plane of area, or POA). The small amount of power generated by the system when all beam irradiance is blocked is from the diffuse component of the irradiance. To completely block all sunlight from the array in a given time step, you would need to set the beam irradiance shading for that time step to 100%, and also enable sky diffuse shading loss and set the diffuse shading to 100%.
Best regards,
Paul.