After joining the modern world and finally moving the theme of my wordpress install to something other than one of the defaults I managed to find one I quite liked the look of. However after playing with it for a couple of days I realised that it had broken the excellent SyntaxHighlighter-Plus plugin.
Not a problem I thought, I’ll just find another theme that does work with the plug in. After about six or seven other themes that broke in exactly the same way it became clear that I would have to do a bit more digging. After much googling I finally found the answer buried in the comments of a blog post.
The long and the short of it is make sure that your theme calls
< ?php wp_footer(); ?>
before the end of
< \body>. This is usually done in footer.php
After all that it turns out that SyntaxHighlighter Plus has a FAQ and this answer is contained therein. Doh!