If you access a core value from Setting, such as host_name from a plugin's init.rb, then the plugin's settings will not be properly loaded.
To reproduce, create a simple plugin that does something like:
myurl = Setting.host_name
and then add in some settings
settings :default => {
'myvar' => 'myval'
}, :partial => 'settings/mysettings'
And then try to access the configure page from Administration / Plugins. You can also go in to the console and try to access Setting.plugin_#{your_plugin_name} here -- you will see it is not available. Meanwhile, all aspects of your plugin work fine, other than the settings and anything that tries to reference the settings.