I noticed two issues that are keeping the plugin from working:
When the home directory (WP_HOME) is different from the WordPress application directory (WP_SITEURL), w3-total-cache mistakenly looks for the "core" .htaccess inside the WP directory.
When the content directory location (WP_CONTENT_DIR) is outside of the WordPress application directory, w3-total-cache, doesn't find it; instead it puts its content files inside {WordPress application directory}/{name of content directory}.
I made a few changes that seemed to get it working, but they're hardly tested so far:
http://pastebin.com/m4Y8rkPE (diff)
I hope these can get fixed soon so I can use this terrific plugin. :)