I'm aware of the special character encoding required for '%' characters to work through the console version, both manually typing through the console and reviewing the .Net library output to the console it appears as far as I can tell that the special characters have all been properly encoded and WinSCP's interpretation of the encoded characters seems to be at fault.
Known conditions for this being an issue:
WinSCP version 5.2.5 beta or higher (5.2.4 beta and lower work fine back to 5.2.1 at least)
.Net library usage / console (WinSCP.com) usage
actual FTP or FTPS-TLS connection
Windows 7 / Windows 2008
Visual Studio 2010 / .Net 4.0