OK if you have the syntaxhighlighter plugin installed it is double encoding for TinyMCE which if you are not using screws this up majorly.
just comment out the support for TinyMCE
// Account for TinyMCE
//add_filter( 'content_save_pre', array(&$this, 'TinyMCEDecode'), 8 );
//add_filter( 'the_editor_content', array(&$this, 'TinyMCEEncode'), 8 );