We ran into this same issue. For those in the future, here is the fix:

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It tells you how to configure the options in the Advanced Options menu to support JUNOS devices.

Please post a log file. Or try SFTP instead SCP (with 3.0 beta only).

Is it possible to login into a Juniper router (BSD based) and SCP a file from it? I have tried to and no luck. I get the following error:

Can't detect command return code.

I looked at the logs and I see that the connection is successfull, however when you log into the router you are not at the shell prompt, instead you are at the CLI and most manually start the shell. So how can I change the prompt that WinSCP receives from the router? Thanks.