Ended up having to include the full path of the folder from the destination server (not the user mapped one) for the put command to upload to. Not sure why that fixed it but it did.

When we upload files to an SFTP site using a private key, the transfer works in the GUI. When trying the transfer using a script it errors out, The errors received are "Cannot create remote file", "Permission denied", "Error code: 3" and "Error message from server (US-ASCII): Forbidden". It appears from the logs that WinSCP is attempting to change the timestamp. We have tried the -nopreservetime, -nopermissions and -transfer=automatic switches on the put command in the script with the same result. The vendor who owns the SFTP site had verified the user has permissions to allow uploading the file (again, it works in the GUI).