It alerts on the installer, screenshot attached. Portable app is fine.

SmartScreen is kind-of a black box, but I know it checks the certificate that signs an installer (or any executable, maybe) against some online database. If you generate a new cert, people will start getting the error until enough people have allowed it to run (establishing some "trustworthiness" for the certificate). It may do other things, but I only know that much because it happened not too long ago with git for windows, though that only took a day or two to clear up iirc.

I also started having this issue both at home and at work.

I just went in to the settings, un-checked and then re-checked "Hide Screenshot Captor Window," accepted the settings, and hid the main window from the tray icon context menu... now it's fine.

One thing that would have helped me (maybe) is having "Hide Main Window" available in the main window's own View dropdown, though this may have been because (I think) after simply closing the main window it remained minimized.

Is it possible something changed with the settings in the latest version that inadvertently un-set "Hide Screenshot Captor Window," requiring it to be toggled off/on in the GUI to take effect again?