From the Support page: Settings not in Data directory - Currently, FileZilla stores its settings in FileZilla.xml in the filezilla directory as opposed to the settings directory.
From FileZilla forums, posted by botg (Site Admin) 2006-03-30 19:15:
There's is an undocumented commandline switch for FileZilla to specify the location of the configuration file: /config
Example: FileZilla.exe /config "c:\foo\bar.xml"
http://filezilla.sourceforge.net/forum/viewtopic.php?t=2087
Wouldn't this a solution to the problem?
Regards,
Manfred Staudinger