Syntax Highlighting in Code Samples

Title: Syntax Highlighting in Code Samples

I'm trying to get the syntax highlighting stuff to work but I'm running into a few problems:

1. My callouts are not working. They produce errors and the graphics don't show up in the code listings.

2. Places where I've added emphasis elements to my code listing to callout a particular line are creating errors. The samples are output but, they are wrapped in things like <em><code>outputDir</code></em>.

What did I miss in my set up?