"just re-upload all index.php and index.html files on your account and it will go away."
I tried re-uploading the index.php on my site but the message is still there.
If you are using a script you didn't write, some of them have an index page in the main directory that loads a template index file. I know that wordpress just includes an index.php from the directory of the defined theme. You'd need to fix that index file too.