I have the latest version of WordPress and Ultimate Security Checker. My client is using Yahoo hosting, which isn't the best in the world but I have figured out how to work around most issues.
When I run the security checker, I am getting an error message 'your .htaccess is unsecured. Yahoo doesn't allow for .htaccess files, so I don't have one to be unsecured.
Any recommendations [other than switching host providers]?
There have been a few hiccups with this plugin, but for the most part it has been smooth sailing. And any issues I have had were resolved with updated versions of the plugin.