Yes. If I've had the time, I would have prefered to package a proper update script, that transfer all "old" settings to the new layout in gconf. I don't have much time so I prioritized a release instead with more solid software and ability to change the URL opened based on SSID.
My guess is that the install-script contains an incorrect key - the application uses only one gconf "root" path/directory, which is /apps/maemo/wifi_assistant.

Yes, you've just identified a bug and I verified that the install-script uses an incorrect path - thanks a bunch!
(I'll write a fix now right away, but I can't push publicly until a new SSL certificate is in place for vcs.maemo.org (version control system) - the certificate expired on new years eve and although reported some time ago it's still not fixed ...)

As a side-note, I'm "shutting down" the garage page in favor of http://wiki.maemo.org/WifiAssistant