Thanks for your reply.
I'll provide the source here, as the page is in development and not ready to be given out yet, sorry:
This is generated by
<link rel='stylesheet' id='shadowbox-css-css' href='http://example.com/wp/wp-content/plugins/shadowbox-js/shadowbox/shadowbox.css?ver=3.0.3' type='text/css' media='screen' />
<link rel='stylesheet' id='shadowbox-extras-css' href='http://example.com/wp/wp-content/plugins/shadowbox-js/css/extras.css?ver=184.108.40.206' type='text/css' media='screen' />
<link rel="EditURI" type="application/rsd+xml" title="RSD" href="http://example.com/wp/xmlrpc.php?rsd" />
<link rel="wlwmanifest" type="application/wlwmanifest+xml" href="http://example.com/wp/wp-includes/wlwmanifest.xml" />
<link rel='index' title='example.com' href='http://example.com/wp/' />
<link rel='next' title='news' href='http://example.com/wp/news/' />
<meta name="generator" content="WordPress 3.1.3" />
<link rel='canonical' href='http://example.com/wp/portfolio/' />
This is the gallery that's created using a custom filter:
<div class="gallery"><ul class="clearfix"><li><a href='http://example.com/wp/wp-content/uploads/2011/06/Image.png' rel='shadowbox[sbalbum-13];player=img;' title='Image'><img width="185" height="119" src="http://example.com/wp/wp-content/uploads/2011/06/Image-185x119.png" class="attachment-thumbnail" alt="Image" title="Image" /></a></li>
As you can see, the markup is being manipulated by adding the rel attributes, so something must be working.
However, the shadowbox.js file is completely missing. The l10n.js file doesn't have anything to do with it either.
wp_footer() doesn't output anything either.
I have the default settings, image links is true and smart loading is off.
I hard-coded jQuery to be always embedded from google apis, I don't think that makes a difference though.
I hope that's enough information.
Thanks for your help!