Please attach a full session log file showing the problem (using the latest version of WinSCP).
To generate the session log file, enable logging
, log in to your server and do the operation and only the operation that causes the error. 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.
Though the problem is likely with the server anyway. WinSCP is the possibly the only widespread SFTP client that actually follows the specification by normalizing the entered paths ("get real path") - If the server has problems with that, you will have problems with WinSCP, but not with the other clients. That does not mean it's WinSCP fault.