Drupal : How to remove the  and  tag from content when using syntaxhighlighter
I can't answer this 100% but my first hunch was "hrm, filter ordering" and look, the project page draws your attention to:


  Very important!!!: ordered the input format filters as follow:
  
  
  HTML filter or Wysiwyg filter or whatever HTML filters you use. They must come before. 
  Syntax highlighter. This come after any and all filters that can modify content input.
  Line break converter. This must be after, If you see &lt;br/> at the end of every line in your output, then you know what's wrong.