Starting MariaDB 10.0.6 with TokuDB gives ERROR 2002 (HY000) but socket is working correctly

Upgraded to MariaDB 10.0.6 today (via aptitude upgrade) and configured the newly available TokuDB engine as my default engine, after changing the configuration file I restarted the server with service mysql restart. The server restarted normally but the following message was printed to the console after the restart finished (and blocked the prompt).

root@s1:~# ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (111 "Connection refused")

The funny part is that I simply hit Ctrl + C and type mysql -u root -p and connecting to server works as expected. Same goes for my PHP application that uses mysqlnd to access the database. No problems with anything, just that awkward error message on the prompt.

I attached my complete my.cnf file.