You right. On Windows, IIS manages the web application. While on Linux there is a service for ScadaWeb.
The Administrator app sends a command to IIS to restart. Sometimes it takes a long. Even if you run the same command from a command line, the result would be the same. For now, I have no idea how to fix that programmatically. As for me, I open IIS management console and restart the web app using it. There is no delay in this way.