Please attach a complete session log files for both scenarios using the latest version of WinSCP.
Using WinSCP 5.7.6 Build 5874
Running on Windows 2012 R2
Problem was not caused by software upgrade
Have created a new set of SSH2 RSA keys, logged into the server with the automated user account.
Have passed those keys to the vendor to install on the server on their end
Have manually attempted to connect to ensure host key is cached on server
Have recreated keys with both PuTTY and OpenSSL
My personal account is able to connect via command line, PuTTY and WinSCP
Automated user account cannot connect at all - "Server Refused our Key" error
Have confirmed that host RSA key is identical regardless of which user is logged into our server
SSH key private file location and user name are passed identically in WinSCP
Why is the Windows server user (who is logged into the server) even a factor here?