This is my .tm_properties which does exclude directories from the left file panel
excludeInFileChooser = "{$exclude,templates_c,*.tpl.php,mobile/build}"
excludeInFolderSearch = "{$excludeInFolderSearch,fnt,chatbot,cached,img,images,templates_c,mobile/build,lib,mobile/archive,mobile/touch,googlesitemap*.xml,*.sql,*.gz,*.tar,*.swf,*.min.css,*.min.js,*.tpl.php}"
excludeInBrowser = "{$excludeInBrowser,.tm_properties}"
Not 100% sure, but all I can suggest is perhaps the $special_vars only apply to the block they are in?
Also note my excludeInFolderSearch includes $excludeInFolderSearch as the first entry, likewise for excludeInBrowser