There can be different reasons for this issue. The best way to figure out the issue is "check your webserver log" which will be "/var/logs/[apache or nginx]/[the log file name configured in virtual host]".
In this case, the error message is:
FastCGI sent in stderr: "PHP message: PHP Fatal error: Call to undefined function apc_clear_cache() in /path/app/code/community/Buric/Apc/Model/Observer.php on line 13" while reading response header from upstream, client: 188.8.131.52, server: www.mydomain.com, request: "GET /index.php/admin/cache/flushSystem/key/a2a654d657aafaa937e8acdfba5540af/ HTTP/1.1", upstream: "fastcgi://127.0.0.1:9000", host: "mydomain", referrer:
Means, the magento plugin Buric_Apc is unable to perform the apc cache flush which is because, the APC module is not enabled in php or not installed on server