I see a couple of things but they don't relate to your problem. First, the Order directive should come before the Allow from directive. You also only need the word "from" once. now getting back to your problem. As I said this is a new one on me bcause I don't know what could be causing just the directories with .htaccess to be hidden. Have you tried deleting the .htaccess file to see if it shows up in the index again? If not then it has nothing to do whith .htaccess. I would look more at the directives that have to do with displaying it. For example, are those directories in the list after the directive "IndexIgnore"? It may be something simple but right now, nothing comes to mind on what could be causing that.