Version 0.9.2.7 does not work with a cPanel site or a site powered by CloudFlare

After using the plugin on two sites, I can testify that the new version does not work in two separate situations:

1: Any site using cPanel and WHM as a backend: The new version of W3C Total Cache will try to overwrite the root index.php file upon installation with 777 permissions (all users have full read/write/execute permissions.) This is a common website attack tactic and cPanel/WHM will block the website from running the insecure web page and displays a 500 Internal Server error. Uninstalling W3C Total Cache will not help: the index.php file will still have the 777 permissions. As a workaround, you can just reset the permissions on the file to 400.

2: Any site using CloudFlare: CloudFlare is a reverse proxy optimizer that W3C Total Cache can integrate with. The new version’s integration does not work. I receive error messages about connection problems when trying to activate this feature. Also, all of my CSS and HTML formatting is messed up. Disabling the CloudFlare feature does not work. I had to disable the plugin entirely.

I don’t even know if the new version fixed the problem in 0.9.2.6 with backup plugins like BackupBuddy not working with this plugin.

http://wordpress.org/extend/plugins/w3-total-cache/