On a multisite installation, using cloudfiles CDN, i am getting errors that the [prefix]_[blog_id]_w3tc_cdn_queue tables do not exist. After updating the plugin I got the same error for the table wp_w3tc_cdn_queue, but after saving w3tc settings (if i remember correctly) it seemed to create that table. However, it does not seem to ever create the multisite tables (ie wp_3_w3tc_cdn_queue, wp_4_..., w3_5_... etc). I have tried this with using a single config file and with using separate config files for each site.
Hope that's a clear enough description.