That particular dialog has been the same since Windows 10's launch, though it is "adaptive" in that as the reputation slowly builds it will show the Run Anyways button at something like "medium reputation".
Ahh, that explains it. I had a screenshot of the SmartScreen dialog on my download page. After releasing a new version last fall, I noticed the dialog changed to the hidden Run Anyways option. My error, apparently, was including the major version number in the setup file name. When that rolled, the reputation reset.