If I select the option to create the index.php files in the various folders, then update the settings, I get the following error at the top of every admin page:
Warning: file_put_contents(/home/user/public_html/website.com/readme.html) [function.file-put-contents]: failed to open stream: Permission denied in /home/user/public_html/website.com/wp-content/plugins/wp-security-scan/res/inc/WsdSecurity.php on line 679
And it stays there until I disable the plugin. Reactivating the plugin brings it back. But deleting it and then completely re-adding and activating gets rid of it. But it also erases all the settings, and I still get a warning, within the plugin, about not having the index.php files in the various folders. Any ideas what's causing this?