Yes, the DIA-NN command line is creating a document using the same settings as the last document that you had open in Skyline.
That is, when it passes the "--new=" argument to SkylineRunner.exe, that creates a new Skyline document using settings that came from the last file you had opened in Skyline.
It would probably be better if DIA-NN used the "--in=" argument to open an existing Skyline document.
One thing that you could do to get this to work is run Skyline and use the "Settings > Default" menu item to change the settings back to Skyline's defaults and then exit Skyline.
Then, when DIA-NN creates a new Skyline document it will use the default settings instead of the settings that you are using now.
A different thing that you could do in Skyline is to go to "Tools > Options" and click the "Clear all saved settings" button on the "Miscellaneous" tab. This is a more drastic solution which would result in more settings being reset, including whatever custom reports you might have designed. The "Settings > Default" menu should be sufficient to fix this problem.
If this does not fix the problem then you should send us your files and we can try to figure out what is going wrong.
You can package everything in a .zip file and upload it here:
https://skyline.ms/files.url
(I'm not sure exactly which files we would need to diagnose this problem. Maybe everything in the "E:\Shubham\DIANN\results" folder)
-- Nick
Skyline failure.txt