Asterisk 1.4 + asterisk GUI question

I have an existing asterisk 1.4 (debian) install running. I have checked out the current GUI, and installed in on the server. I am able to get the GUI to load, but it looks like none of my existing .conf files are getting loaded - for example I have several trunks defined in iax.conf, but the GUI says no trunks are defined.

Does the GUI not work with existing configurations?