Hi,
Just an FYI for anyone else in a similar situation. Running W3TC 0.9.2.9. I'm getting the 'It appears Minify URL rewriting is not working.' error message. However minify is working. In fact I don't see any issues with plugin functionality at all.
I am running WP admin over SSL with FORCE_SSL_ADMIN set to true. If I set it FORCE_SSL_ADMIN to false, the error message disappears.
Cheers,
Steph.