Jason, we experienced a similar issue with replicating the w3tc settings across servers. We have a dedicated wp-admin server which is locked down via VPN which saves content and settings for the load balanced front end servers.
We setup a frequent rsync of the w3-total-cache-config.php settings files (including /wp-content/w3tc/*
) from our wp-admin server to the front end servers, it works pretty well.
One of the advantages we have found with having the w3tc settings outside of the DB has been replicating them (via file upload) with our test servers which have different databases, its good to have the settings separate from content.
Hope this helps
Jeremy