Here are my settings
and you can see in the source code that I still have lots of css & js http://sfstock.net-commerce-solutions.co.uk/
<link rel="stylesheet" href="/templates/t3_bs3_blank/local/css/thee="text/css">
<link rel="stylesheet" href="/templates/system/css/system.css" type="text/css">
<link rel="stylesheet" href="/templates/t3_bs3_blank/local/css/themes/socksfox01/template.css" type="text/css">
<link rel="stylesheet" href="/templates/t3_bs3_blank/local/css/themes/socksfox01/megamenu.css" type="text/css">
<link rel="stylesheet" href="/templates/t3_bs3_blank/fonts/font-awesome/css/font-awesome.min.css" type="text/css">
<link rel="stylesheet" href="/templates/t3_bs3_blank/css/custom.css" type="text/css">
<link rel="stylesheet" href="/modules/mod_redshop_cart/css/cart.css" type="text/css">
<script async="" src="//http://www.google-analytics.com/analytics.js"></script><script id="facebook-jssdk" src="//http://connect.facebook.net/en_GB/all.js#xfbml=1&appId=107745475910498"></script><script type="text/javascript" async="" src="http://www.google-analytics.com/ga.js"></script><script src="/media/system/js/mootools-core.js" type="text/javascript"></script><style type="text/css"></style>
<script src="/media/system/js/core.js" type="text/javascript"></script>
<script src="/media/system/js/caption.js" type="text/javascript"></script>
<script src="/media/system/js/mootools-more.js" type="text/javascript"></script>
<script src="/plugins/system/t3/base-bs3/js/jquery-1.11.2.js" type="text/javascript"></script>
<script src="/plugins/system/t3/base-bs3/js/jquery.noconflict.js" type="text/javascript"></script>
<script src="/plugins/system/t3/base-bs3/bootstrap/js/bootstrap.js" type="text/javascript"></script>
<script src="/plugins/system/t3/base-bs3/js/jquery.tap.min.js" type="text/javascript"></script>
<script src="/plugins/system/t3/base-bs3/js/script.js" type="text/javascript"></script>
<script src="/plugins/system/t3/base-bs3/js/menu.js" type="text/javascript"></script>
<script src="/plugins/system/t3/base-bs3/js/nav-collapse.js" type="text/javascript"></script>
<script src="/modules/mod_redshop_search/js/search.js" type="text/javascript"></script>
I'm on T3 Blank Bootstrap version 2.2.1
Joomla! Version Joomla! 2.5.16 Stable [ Ember ] 06-November-2013 22:30 GMT
Joomla! Platform Version Joomla Platform 11.4.0 Stable [ Brian Kernighan ] 03-Jan-2012 00:00 GMT
And I have tried with ThemeMagic on & off.
