phpMyAdmin session timeout is controlled through two parameters. The first one can be found in /etc/php5/apache2/php.ini. It is called session.gc_maxlifetime. The other one can be found in the phpMyAdmin configuration file often named /etc/phpmyadmin/ The name of the parameter is LoginCookieValidity.

The one located in /etc/php5/apache2/php.ini superseeds the one given in /etc/phpmyadmin/ if it is smaller.

phpMyAdmin might also have a local php.ini that can override /etc/php5/apache2/php.ini.