When we clear the cache, the way we do it is to schedule an event in WP to run immediately, then we hit the /wp-admin/admin-ajax.php URL so that the scheduled event will run.
So if you're seeing this it's possible that the request where the server connects back to itself does not execute as it should, even though the cache clearing has been scheduled.
When you manually clear the cache, we don't use the scheduling mechanism, but clear the cache while you wait, that way we can return the real-time stats to you that you see in the result.
So do the following test: Do whatever action you expect will clear the cache. Then hit your site's home page in a browser. Then wait a minute. Then check if the cache was cleared.
Hitting your home page will also trigger the scheduled clearing of the cache that should be triggered by your server connecting to itself.
Hope that helps - just trying to give you an internal view of what we're doing in the hope of helping you diagnose the issue.
Regards,
Mark.