WinSCP compares files by last modification time. Next version will allow comparison by size too.

You may adjust time zone difference between your server and client on SCP tab of login dialog. Or use SFTP instead , which does not suffers with this problem.

How does the compare directories command decide if files are different? In my application, the remote server is in a different time zone. Files that I copy from my PC to the remote server are listed with different times (shifted by the time difference between my location and the server location). These files are marked as different even though they are the same content.