There indeed do not seem to be any difference in login details between the logs.
But I can see that the IP addresses the hostname resolves to are completely different between the logs. Is that expected? Did you try connecting in the script explicitly to the IP address that the GUI uses?

Also WinSCP version is different. While I do not expect this to be a problem, try using the same version anyway. Can you ask "them" to try to connect with UI from the SSIS machine?

Hi – I have tried many of the solutions mentioned and I cannot get this working. It seems to point to the password, but from the logs I have no idea. It mentions the stored password and the entered password which is odd for the logs to do both.

I am attaching the logs and script as a private file. I tried using /LogLevel=2* but saw no difference in the output. The behavior of this app is quite unpredictable from one machine to the other. I don't have access to the SSIS machine, I can just modify the batch files that pass the parameters. I would like this to just authenticate without any of the stored data of the app.