this is a topic for somebody who may face similar thing in future. Once you try to schedule task in Windows using executable that was compiled with PyInstaller with option -noconsole and trying to use subprocess.check_output it does not work
Funny thing that if you call .exe directly then it works perfectly fine. However if you schedule a task or try to wrap execution into batch like:
C:\git\backend.exe -p C:\Users\settings.json
then it fails without any error code.
Only thing one can found is in tasks event log is error code: 2147942401