You can do this :
Navigate to C:\Users\[User Name]\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\startup
Here, create a shortcut to the desired application.
Open the properties of that shortcut, and go to the "Shortcut" tab.
You have a drop down menu. Click it and choose "Minimized" and click the OK button.
The choices here are "Normal", Minimized" and "Maximized"
This works on ANY version of Windows, from Windows 95 and NT 3.0 up to Windows 10.
By the way, you really DON'T want to run it as a service. You want only the genuine services to be run that way.
BUT, MSE 2016 is now obsolete and it may be why it no longer start as it used to do. You need MSE 2018 of switch to some other anti-virus application.
The best way to correct your problem is to :
1) Uninstall your actual version.
2) Download the current version and install it.
3) Make double sure that it's set to automatically update itself and not only it's viral database.
4) Make sure that Windows updates is set to automatically install all updates for Windows and other products from Microsoft and can be run by all users.
You may also want to look if there is an option to "Search for updates". If you find it, or something similar, you can use that. It will look to get the latest version, download and install it for you with only minimal user intervention. In this case, points 3 and 4 above still apply.
I must congratulate you for providing as much information as you could and to give detailed information about your situation and problem. It's always better to provide more information that needed that leaving out needed information.