How do I get Drupal to load a node instead of looking for the index.php outside of drupal in a subfolder
You'll need to remove the original file, or make it unreadable by your webserver. Drupal is basically a big 404-handler; if the file exists it will get loaded before the webserver looks for the default index.php which then bootstraps Drupal.

That, or check to make sure you don't have APC or similar opcode cache installed.