Please post a session log file showing upload of a single file, both from GUI and command line.
I believe I know what the issue is. Since our FTP server is behind a NAT the WinSCP client (CMD-LINE) is not seeing the IP used to initiate the connection for the Data Channel. This is only applies to the CMD-Line version of WinSCP, because in the GUI version the logs are showing that it is using the original IP and not the IP the server is recommending back to client, which is the private.
My question now is what, if any, switches can I use to tell the command line to use the same IP for both the Data and Control Channels? For example the other product i mentioned has -natpasv as a switch to make it use the same IP. Does WinSCP CMD-Line have this capability?