After a lot of tinkering, I just figured it out (kind of). It will only execute the PHP script if it is on the index of the subdirectory and if you try to go to the subdirectory (apps/ServerStatus/ works but apps/ServerStatus/index.php doesn't). It works if you go to any PHP script on the server root. It also executes any file is it is executed with JavaScript.
So the new question is, how do I make it so it executes files in a subdirectory if it isn't named index.php, too?