In the latest version I'm using (5.7.5), WinSCP started to offer uploading of files, that was modified, but the original connection has been broke.
So it asked if I want to reconnect to upload it.
It is a really nice feature, but when using mulitple SCP connections, it mixed the files up, and uploaded them to wrong server. It never happened with live connections, only when it has to reconnect, but with that, it made a few mistakes last day.
It happend on Windows 8.1 (x64), using WinSCP ver. 5.7.5, using multiple SCP and SFTP connections.