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Using phpmyadmin, on Debian Jessie 8, installed thru the official repository with apt-get. There is a config folder in /etc/phpmyadmin where the config.inc.php is situated. Editing /etc/phpmyadmin/config.inc.php worked for me.
how did you install phpMyAdmin? If you do it via yum, then the config.inc.php is taken care of, but if it was manual, then you need to make sure config.inc.php is placed in the top-level directory of phpMyAdmin (e.g. /usr/share/phpMyAdmin). Permissions don’t seem to matter, as mine is root:root and still works.
I’m having the same issue with nginx, the config.inc.php it’s completely ignored.