To workaround this problem, we have to use an "ls" right after the "put" command. To me it seems, that the connection is closed "too early", causing the transfer to fail in Axway Synchrony Gateway. So the issue is still existing, maybe there was no relation to https://winscp.net/tracker/489 ?
Is it possible to sent some details to you? Are you interested?
Please start a new thread and attach a complete session log file.