But that didn't work out, when I run the winscp.exe I don't see any session information. I believe because when I run the installer, I have to run it as an administrator so the registry keys are created under the Administrator account, when I run the software I'm running as a regular user, so I'm not seeing the session information in the registry keys.
That's true, if you are actually using a different administrator account for installation. But typically, you use the same account, just with elevated privileges.
So my next attempt was using an .INI file like:
Why are you using
WinSCP2.ini? The INI file has to have the same (base) name as the executable, i.e.
Also make sure you store the INI file to a writable-location [unless you really want to read-only]. I.e. to user profile folder. But with that you'll have the same problem as with registry path, if you are really using a different administrator account.