Not sure what this “setup.exe” does, but it’s probably a safe bet that the /S parameter is not sufficient to make it I stall silently. It’s likely trying to prompt for some info like “click OK to continue”.
Executable installers on Windows don’t follow a standard convention. Each software vendor determines their own command-line parameters for a silent setup. You’ll need to check with the vendor documentation, or perhaps try running ‘setup.exe /?’ from a command prompt to try and determine the command-line parameters you need.