Vista redirects all files, which were written outside of users home-directory, to a special dir, that is called "VirtualStore" (%appdata%\VirtualStore), because filewritting outside of usersdir is not allowed to restricted users. Registry-entries, that were written to HKLM-Tree are redirected to HKEY_CURRENT_USER.
That is a temp. mechanism from microsoft to ensure, that "non-vista-compatible"-applications are working further on. But ms intends to disable it at any time...
I think, you have two options now:
1. "Rerun" flashfxp-setup and select, that flashfxp should store your settings in your users %appdata%-dir
2. Perform your edits in %appdata%\VirtualStore-directory (or was it local-settings-dir? dont know...)
http://windowsconnected.com/blogs/je.../12/19/86.aspx