I always use Inno Setup for packaging and publishing. Users download the application using a link for example: https://oursite.com/codesigned/mysetup.exe
Till now,
I think this is normal behavior. When your software collect enough "likes" = downloads or installs the SmrtScreen will automatically turn off this message.
It is really annoying feature because with every software release you need to wait appropriate time while the software become "popular" and it is recognized as safe (no certificates or antivirus methods can solve it).