Yes, it does start normally from the shell but it doesn't work if I use it to load a saved preset file.
Code:
Font FROM Saved Font.pre USE
And I'm using a modified version of this
http://aminet.net/util/wb/themesaver.lha
Which basically works by saving/loading certain preset files. But I just copied the original Font Prefs to C: so it has a higher priority. It's not perfect but it works.