I would check if something in the signing process is going wrong, refer to this (very long) SO thread: https://security.stackexchange.com/questions/109629/deprecat...

We actually switched certificates (from StartCom to Globalsign) and the signing was wrong at first, so the message kept showing. When we fixed it, it went away immediately, even though certificate and author name changed...

Here's the article:https://blogs.msdn.microsoft.com/ie/2012/08/14/microsoft-sma...

"Programs signed by an EV code signing certificate can immediately establish reputation with SmartScreen reputation services even if no prior reputation exists for that file or publisher."