Please attach a full log file both from GUI and script showing the problem (using the latest version of WinSCP).
To generate log file, use
/log=path_to_log_filecommand-line argument. Submit the log with your post as an attachment. Note that passwords and passphrases not stored in the log. You may want to remove other data you consider sensitive though, such as host names, IP addresses, account names or file names (unless they are relevant to the problem). If you do not want to post the log publicly, you can mark the attachment as private.