Drupal 7 Syntax Highlighter not applied when logged in as user or admin
Well, since nobody seems to want to answer my question, I will provide my solution to the problem. As I have discovered. Drupal do not load all javascripts, go figure why.

So, what I did is go to the admin panel. In configuration/performance you can aggregate all javascript files into one big file which apparently helps minimize server requests. When I did that, it worked. The syntax highlighting is now applied all the time, with a nasty side effect.

I got my code-hightlighting effect working but now, the wysiwyg shows up in comment's textarea field with a background that matches my websites... How unfortunate!