www.stunnel.org is a SSL tunneling program, orginally for Linux but there's windows binaries there that works perfectly fine.
You simply set it up to listen to a port locally, and tunnel to a remote SSL machine (it could be a SSL IRC server or FTP or pretty much whatever), then connect to the configured port with your client (would be FlashFXP in this case then) and you got a SSL connection with the remote server :-) It's based upon OpenSSL.. For Windows SSL FTP servers, check out the Serv-U 4 beta (SSL is the big news for Serv-U 4). Good luck!