Well, you are the first one who have ever reported this. So it must be something about the way you use WinSCP.

How exactly do you upgrade WinSCP? How do you run WinSCP for the first time? Do you let the installer start WinSCP? Or do you run it manually (how)? Where do you have your WinSCP configuration stored?

After installing, it opens a new WinSCP 'Login' window with nothing in it but 'New Site..."

Just closing it and re-launching it brings back all the saved connections, but since there's no warning about this little quirk; the first time anyone upgrades, they're going to be temporarily stressed out and infuriated at having to start over and re-enter all their server configs.