So I found out what was messing up highlightjs when dealing with comments. When Atto puts in a preformatted section, it will put in <BR>'s every time you do a soft enter (holding shift and pressing enter). It puts in a </PRE><PRE> every time you press enter without shift. Well these extra tags screw up the hightlight script.
if (x == 3)<br> BAD NEED TO REMOVE THESE BR's
// I love pizza<br>
So I write some jquery scripts that scrub out the <BR>'s and replace them with \n's. That makes the highlighter happy. I haven't been able to replace the </PRE><PRE>'s because i'm not that gifted with jquery. They are the containers and I'm not that smart. So basically you have to go in and manually remove hard returns.
Anyway, i'm pretty happy with how it looks now. I've attached it below: