You are trying to use the Restart button in Zend Server UI and the Apache restart doesn't happen, for example, after some PHP settings change. The same may happen, when you deploy an application through the Zend Server UI or through WebAPI - the files are put into place, but the changes never take effect, because Apache is still using pre-deployment configuration.
At the same time, manual restart (e.g.: sudo service zend-server restart) works correctly.
Zend Server on Ubuntu/Debian Linux
One of the most likely causes of such behavior is incomplete startup environment of Apache. During Zend Server setup the installation script makes sure that Apache starts in a correct context by adding the following line to the file /etc/apache/envvars (at the very end):
Sometimes this injection is removed at a later point. The most common cause - restoring the Apache configuration (or part of it) from a pre-Zend-Server backup. This may be a result of manual maintenance or a side effect of some automatic configuration management tool.
This line is essential for some of Zend Server's functionality and needs to be added to /etc/apache/envvars, if it's missing in your setup. In case you use some third-party software to manage Apache configuration, this line needs to be "white-listed" in this software.