We're running WP 3.0 with a dev build of W3TC from yesterday (7th July). We're having problems, which are possibly to do with our server configuration. I had a dig, and one part of W3TC that isn't working is the w3_get_home_root() function, as used in w3_is_permalink_rules().
We're just getting a $path of '/.htaccess' i.e. it's looking in the wrong place. Our absolute path looks like /home/d/o/domain.com/public_html/ (server is using apache's virtualdocumentroot). Any ideas?