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In hook_flush_caches() there is a piece of logic that checks if it was called by cron. It does this by checking lock_may_be_available('cron').
The problem with that approach, is that it spans across requests. So whenever cron is running, hook_flush_caches() will not flush, regardless of being called from cron or not.
Perhaps a better approach could be to check $_SERVER['PHP_SELF'] for 'cron.php'?