I did some testing.
With WP Cache and Super Cache both enabled, expired files just pile up, never being deleted irrespective of when I set expiry time to.
With the "HALF ON" option set (Super Cache Disabled, only legacy WP-Cache caching) the plugin works perfectly with files being cached and expired files being deleted.
I did test switching "Disable file locking" on with no change to the above findings.
Certainly on Dreamhost and Hostgator servers this is the problem I've seen...legacy cache works and expired files are removed, super cache works but expired files pile-up.