Hello Donncha,
I wrote a plugin "Silence is Golden Guard" which creates empty index.php file at the folders where it is absent and has an "redirect to blog root" option. It puts
Options -Indexes
directive into .htaccess file also.
If I put such index.php file as
<br />
<?php<br />
// This file was created automatically by Silence is Golden Guard plugin<br />
header("Location: http://www.shinephp.com");<br />
?><br />
to the /wp-super-cache/plugins/ folder any call to blog root URL or /wp-admin/ ends with browser error, e.g. for FireFox "Firefox has detected that the server is redirecting the request for this address in a way that will never complete."
Is that normal behaviour for your WP Super Cache plugin? Or it could be resolved?
As a temporal decision I check if the '/wp-super-cache/plugins/' folder exists and WPSC is active, then I put just empty index.php file into /wp-super-cache/plugins/ without redirection directive.