We use a setup where WP has its own directory. The new version of the plugin is displaying a notice to create a file called "w3tc-wp-loader.php" for Minify and support requests to work.
We use Capistrano for deploys, which creates a new path for every release, and changes the location of the wp-load.php file with each deploy. i.e.:
If I put a relative path to wp-load.php file in w3tc-wp-loader.php, it works, but W3TC keeps displaying the notice.
Hopefully you can fix this in a next release of your excellent plugin.