I'm using the latest version of both WP and the WPSC plugin.
My site's installed in a sub-directory: mydomain.com/site/ however it's being served from the root of the domain: mydomain.com
I've just updated my HTACCESS file and it showed me a warning:
However after checking both files, the rules have in fact been added to the correct HTACCESS file.. the one in the ROOT directory, not the one in the sub-directory.
Either I've worked too hard today and I'm confused, or you've now fixed this issue but forgot to remove this warning message from the back-end. Just thought I'd let you know.