Hey @andremart
Welcome to the forum and thank you for using FFAStrans (webint)

Sure you can just install it as a service, then you don't see the application. But make sure the install files are local (e.g. on C drive) instead of on a network drive. Also after installing the service, you'll need to set the service credentials to some username/password that can access the ffastrans installation folder on UNC path. Plus you'll need to change the ffastrans folder to UNC instead of Z: because services don't see mapped network drives.
Alternatively, if you really want to run inside a logged in user session, you can create a batch like
powershell -C start -FilePath "D:\Downloads\webinterface_1.4.0.187\server.exe" -WindowStyle Hidden
Change the path to your path and save as .bat file (startserver.bat). Execute the bat and check if you still see cmd window and server.exe process is running.