well i am not saying it is there, i am saying IF it is there, then thats your problem....
and are you passing a search string when your looking for it, or are you doing it manually....if doing it manually, forget about it, and do a search....cause its very easy to overlook things....
so either open the file either in a graphical or text based editor, or even use 'cat' in the terminal passing 'grep "Files ~"' just don't do it manually....
and like i said, if its not there, then its not there....ew'll have to keep looking for a resolvement..

also just to give you something else to attempt, just in case the string your looking for does not exist, try the following:

locat DirectoryIndex and change it to index.htm

# The following lines prevent .htaccess and .htpasswd files from being
# viewed by Web clients.
#
<Files ~ "^\.ht">
Order allow,deny
Deny from all
</Files>

and ive copyed the index.htm file in the direcotry and named it index.html and index.shtml