I'd just like to bump that I too have seen this issue. (I also submitted a support ticket through the plugin with less info than I have here.)
Schedule Posts are not getting published with W3TC v0.9.2.9 and WP 3.5.1 as a (subdomain) multisite setup when Object Caching is enabled. Switching to Database Caching appears to work fine (I know they aren't the same).
FWIW,the site is running on an up-to-date, dedicated VPS with APC as the caching method for both the Object & Database caches.
I'd be happy to provide more info or help in any way I can. Thanks for a rockin' plugin!