I've just posted a pre-release of FileZilla Portable 2.2.32. In addition to the usual update of FileZilla, this new release includes an updated launcher (hence the pre-release test). The launcher now stores your settings within the FileZillaPortable\Data\settings directory. On launch, it moves them to the FileZillaPortable\App\filezilla directory so FileZilla can use them. On exit, it moves them back. This way, it automatically works with PortableApps.com Backup without the extra hack that was doing it earlier. And, as with all the other apps, you can now delete just the Data directory to reset all settings in FileZilla Portable (handy for resetting to defaults or making a copy for a friend). Multiple launches are handled correctly as the launcher just keeps track of running instances. The only downsides are that the FileZillaPortable.exe launcher now has to stick around. And, although you can use local and portable copies side by side, the portable launcher won't close until all copies of FileZilla are closed.
Please give it a try and let me know what you think.
FileZilla Portable 2.2.32 Pre-Release 2
UPDATE TO PRE-RELEASE 2 (April 20): The package has been updated to use the new NSIS-based installer along with VLC and Thunderbird. Please try it out and ensure it works correctly with the old menu (1.0/1.0.1) new menu (1.0.2 betas) and standalone.