Updated: Comment #0
According to documentation:
This hook asks your module to clear all of its static caches, in order to ensure a clean environment for subsequently invoked data rebuilds.
We do not invoke data rebuilds by system_cron() but drupal_flush_all_caches().
Remove the invocation in system_cron().
User interface changes
hook_cache_flush() is not invoked by system_cron(). This is also the documented behavior:
This hook is invoked by drupal_flush_all_caches(). It runs before module data is updated and before hook_rebuild().
For 7.x and hook_flush_caches()