<base> element is after <script> elements in Default theme header.php

The 'script' elements contain relative URLs but are before the 'base' element in the html. It looks like they default to using the URL of the previous request as the base URL. Try using something like Firebug and look at the generated URLs used to retrieve the scripts and you will see what I mean. The result is that requests for scripts actually go through the main Skylight code causing Solr requests etc.

Have a look at the stylesheet link, it contains ?php echo base_url(); ?, the script elements need to be coded in the same way.