We have multiple ZF2 applications running on the same server. The ./public/index.php does a require of "config/application.config.php".
Zend\Mvc\Application::init(require 'config/application.config.php')->run();
Once that file is cached for one of the applications, the other applications all hit the same file in the opcode cache. Changing the require a full path using getcwd fixes this issue.
Zend\Mvc\Application::init(require getcwd() . '/config/application.config.php')->run();