Nice to know that you've found the solution, Duncan.
Anyway, I'm including the code for others who might be facing the same situation:
Dim client as Ftp
client = new Ftp()
client.Rename ("/old/folder", "/new/directory")
Please note that it may fail if someone (either you, another FTP user or a different process) has their current directory set to "/old/folder". Also, some FTP servers don't support renaming directories.