First note: ftps, as a protocol, is what happens when siblings marry. Stapling SSL on top of FTP's dual channels is like stapping skis on a dachsund and calling it a sled: it's amazing it works at all. The necessary dual channels lead to numerous nasty and conflicting local "solutions". These work great until they don't, and it's hideously awkward to test with all the different "solutions" that may arise in between your client and a remote server. This makes the mishandling often out of the control of the hands of any one party. Proxies, firewalls, and even client implementations come up with subtle distinctions that break things. So you might be able to get it to work, but I urge you to revisit whether you need it. (I've had good success with WebDAV over HTTPS, for example, which is also built into most of the same clients and only requires port 443 handled normally, not the dual channels of FTPS.)
Second. If you're running an FTPS server, why not use the built-in vsftpd, which supports it as well as can be reasonably well, rather than interweaving Filezilla into the mix? Third. the "lftp" tool is about as sophisticated as you can get for an FTP/FTPS client. It's very powerful, very scriptable, and even works very well for mirroring and websites. Does "lftp" work, rather than the command line "ftp" client itself?
