This question has been answered by sottwell. See the first response.
IndexIgnore */* <Files *> Order Deny,Allow Deny from all </Files>
The .htaccess in the core directory needs a little change - instead of Files *.php, putThanks Susan, I had the same problem and this worked for me too!!
IndexIgnore */* <files *=""> Order Deny,Allow Deny from all </files>