Actually, the developer trunk fixed the issue for me. Thanks!
I seem to have the issue where the origin seems to be the same for both but I still get the error.
WordPress Address: http://localhost/wordpress
Site Address: http://localhost/wordpress
And the plugin adds the following script source:
<script type="text/javascript" src="http://localhost/wordpress/wp-content/plugins/hyphenator/Hyphenator.js">
Rolling back to 4.0 for now.
