I have asked same thing before, and so far the issue has not been fixed. When the cron job is running, W3TC will cause problems to it if the database and/or object caching is active.
My GD Press Tools Pro plugin for own cron jobs (backup, auto tagger and sitemaps) needs to perform database operations (both read and write), and if the W3TC is active with database and/or object caching, these crons either fail or end up with invalid data. As soon as the W3TC is disabled, everything works fine.
Cron jobs don't run as on the admin side, but they have DOING_CRON constant set, and yet, W3TC still doesn't handle that as it should. Database and objects cache must be disabled on any of the admin side pages, on all DOING_AJAX and DOING_CRON executions. From the error logs my users sent me, I see that with both AJAX and CRON calls are routed through W3TC replacement DB class, data received from that class is usually invalid causing all sorts of problems.
Another issue is that those users that run database cache have massive problems with performance, and more than 60% of all SQL queries end up with 'mySQL server has gonne away' message. I have no idea how database cache is actually effective, but making it work as it should is a big problem. I run WP on VPS servers, and whenever I try to use database and objects cache (APC or whatever method I tried), I end up with tons of problems.
Will these problems be fixed any time soon, this is not new problem, this is happening for a long time?
That said, files cache, CDN and other things work great, and I use them on all my websites. Thanks for the great work and great features.