I am seeing HTML comments which show the correct files to look for, but the plugin does not actually put them into the <head> of the page.
I see just this:
<!-- TEMPLATE PROVISIONING CSS: 'global.css', 'ie/global.css', 'page-library.css', 'ie/page-library.css' -->
http://wordpress.org/extend/plugins/template-provisioning/
Aiight I got it. You're using TEMPLATEPATH which will return the theme directory when you're not using a child theme. As many themes are child themes, I'd suggest you either add some more logic to look in both places or use a function like get_stylesheet_directory to get this. If you want help, let me know. I've modified my local version to do the latter.