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Very good, thank you.

I keep getting surprised by all that this tool can do.

It's not about MD5. Note that even your GUI dialog shows both MD5 and SHA-1 for the same host key. It's about host key algorithm.

There's no option to configure preferred algorithm in WinSCP GUI.
But you can use Hostkey raw setting:

Or you can use PuTTY, which allows setting preferred algorithm and import PuTTY settings to WinSCP.
See also

Is there a way to force the older MD5 in the GUI? I've poked through the Advanced Site Settings dialog, but nothing's jumping right out at me.

I need this because I'm supporting a customer who's still on MD5. The multi-key server at my site is an Ubuntu Server running in my Dev environment, but the customer requirement in Prod ripples down to Dev, both GUI and Automation.

Well, I expected a log file from ScanFingerprint method.

What I can tell you so far, based on these logs, is that the server has multiple host keys.

.NET uses an RSA host key, because you've told it so (SshHostKeyFingerprint = "ssh-rsa ...").

While GUI defaults to an ECDSA/nistp256, because it's a more secure host key than RSA.

OK, got it. Here you go.

Thanks for all that you do.

Opening of a session is logged too, naturally.

Hm, now you've got me confused.

How can there be session logs if all of this occurs before any session becomes active?

Re: Server Key Mismatch

Please attach session log file both from GUI and .NET assembly.

Server Key Mismatch

I have found that the automation module returns a different MD5 key than does the UI, using the Session.ScanFingerprint() method. In this case, the key returned from the SDK is the correct one.

SDK: 78:b7:60:ec:c9:51:7b:a8:a5:55:2e:76:ab:08:c2:89
UI: c4:38:c2:a9:c5:87:16:d7:27:67:1d:85:e8:37:d9:9c

1. I'm using v5.13.3
2. I don't believe this was occurring under v5.11.2 (but I could be mistaken)
3. I'm running my app on Win10; the server is Ubuntu Server running in a VM
5. Automation/GUI (both)
6. No error message (except in my app, due to a key mismatch)
7. N/A
8. N/A (problem manifests prior to session start)
9. Code:

Dim oSessionOptions As New SessionOptions

oSessionOptions.Protocol = Protocol.Sftp,
oSessionOptions.HostName = Utils.Registry.ImportHostName,
oSessionOptions.UserName = Utils.Registry.ImportUsername,
oSessionOptions.Password = ImportPassword.Decrypt(Utils.Entropy)

Using oSession As New Session
  Return oSession.ScanFingerprint(oSessionOptions, "MD5")
End Using