The file you attached had some problems with the inverter MPPT input settings. The multiple MPPT input option is only available for systems with one inverter. Your system has 3 inverters, so on the Inverter page I set Number of MPPT inputs to 1. Attached is a modified version of your file with the corrected MPPT inputs.
The results for this file do not show the module deviation from STC loss that you mention. Can you share the 3D shade scene you are using? You can click Export at the top of the Shade Calculator window to save the scene as an .s3d file.
Thank you for the fast answer, then the problem is obviously in 3D shading scene. I am sending you the shading scene and also the weather file that I am using (I am using POA from reference cell, temperature and wind speed)
This looks like it might be a problem with the "POA from reference cell" option. Please try using the "POA from pyranometer" option for now, and we will look into this issue.
It turns out that the POA from pyranometer option requires that the weather file have atmospheric pressure data in addition to the POA, ambient temperature, and wind speed data.
We are investigating this and will update the documentation and error reporting accordingly.