Open [web_root]/libraries/Config.class.php add these lines to the beginning of the load method:
var_dump( $this->default_source); var_dump( CONFIG_FILE); die;
Open phpmyadmin. This is the order of loading the configuration files, they create the $cfg variable, which is the PMA configuration, for me the output was:
'[mywebroot]./libraries/config.default.php' '/etc/phpmyadmin/config.inc.php'
Make sure that the last file that is intended for local changes exists and has the correct permissions. Then get rid of the added lines.
Additional Information
The PMA loads the global configuration into the libraries/common.inc.php:306 file.
$GLOBALS['PMA_Config'] = new PMA_Config(CONFIG_FILE);
Global is an instance of PMA_Config , whose constructor calls the load method. In boot mode, the parameter passed to the constructor, CONFIG_FILE used to load the configuration.
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