Recently, phpDocumentor 1.3.0RC6 was released (1.3.0 stable is coming soon, stay tuned). In this release, I finally got around to fixing the problem with source highlighting and CSS in the HTML templates. If you have been using your own custom template based on the standard distributed templates, you will need to make a few changes. Most importantly, you'll need to go into your options.ini and make changes similar to this:
http://cvs.php.net/viewcvs.cgi/pear/PhpDocumentor/phpDocumentor/Converters/HTML/frames/templates/default/options.ini?r1=1.2&r2=1.3
In addition, you'll want to make sure your style sheet has an entry similar to this:
http://cvs.php.net/viewcvs.cgi/pear/PhpDocumentor/phpDocumentor/Converters/HTML/frames/templates/default/templates/media/stylesheet.css?r1=1.1&r2=1.2
If you based your template off of another of the templates, you can see the exact choices you need by examining CVS of phpDocumentor (the above links can be used to navigate to the template you need)
Happy documenting!