Font Xplorer (released back in 2001) is is not fully compatible with Vista. On Font Xplorer web page, in system requirements section, did you notice "Vista not supported"?
The "magic" is stored in c:\windows\fonts\desktop.ini file. If you delete this file, "magic" is lost and if you restore it with right contents, "magic" is restored.
On Vista, your c:\windows\fonts\desktop.ini file must contain these lines (to restore "magic"):
Font Xplorer writes "UICLSID" (same as earlier Windows versions, as it does not know about Vista) instead of "CLSID", that is why it does not work on Vista.