I think it might be that I didn't restart the server after the automatic install. I don't want to add the "restart-server" url to my install.xml like in dotlrn, as I do not want to keep restarting the server after each account is created. I guess I can just post a message stating that you have to restart the server if the dependent applications have *just* been installed.
Perhaps we could include conditional statements into the install.xml file as well? It could end up having the same functionality as an Ant script.