I think I have found a problem with WP Super Cache cleaning expired files.
I use the mod_rewrite cache. So, when all pages are cached, of course there is not anymore calls to PHP files which could clean something.
So I have deactivated the wp-cron.php call in WordPress to make it manually by crontab.
While I have the cron calls which are working great now with the crontab, the WP Super Cache still not clean the expired files.
The crontab is called every 5 min, and the delay of expired files is 1 min.
I have looked at the plugin code trying to understand how this plugin works. We can see that in wp-cache-phase2.php file, there is the function wp_cache_phase2() wich manage if the current viewed page should be cached or not, and only after that, activating the garbage colelctor.
The problem with this, if I'm right, is that calling wp-cron.php will never do something, because this page is never cached, and since the functions which are activating and scheduling the GC (wp_schedule_single_event) are called only if we are currently on a page which could be cached (if not it's just return false and doesn't move forward), it will never work.
Please tell me if I missed something or what.