I was able to resolve the problem on the 3rd computer by uninstalling with revo. It found a leftover registry keys under class. After reinstalling without ninite and unticking that box in setup, everything is working perfectly.

Happening on 3 Windows 10 (Pro Version 1709 Build 16299.371). Ninite was used to install winscp on these pc's initially.

One computer fails to register ssh links that aren't associated with winscp. If winscp is uninstalled it's like it's trying to access an executable that doesn't exist-nothing happens. I downloaded the setup manually and uninstalled in hopes it takes care of any leftover registry values, but sadly no dice.

I'm using a custom registry entry much like the one you linked here https://superuser.com/q/204066/213663#1165049

I will redownload the setup for these machines and untick that box. Should fix 2 of them.

What version of Windows are you using? This could be happening on Windows XP only.

Anyway, you can opt out of registering WinSCP for protocols in its installer:
https://winscp.net/eng/docs/ui_installer_selecttasks

My custom ssh protocol located in HKEY_CLASSES_ROOT is being overridden. How can I disable WinSCP from handling ssh:// links without uninstalling?