Debian based systems Session killed at 30 minutes in special cron, how to override?

Edit the file /usr/lib/php5/maxlifetime

The value should be in seconds. This file will actually also check your php.ini so I don't know why it wasn't working for you.

This is a question for serverfault.com.

However, change session.gc_maxlifetime in /etc/php5/apache2/php.ini or - if you don't have an apache2 one - one of the other /etc/php5/*/php.ini files. The script /usr/lib/php5/maxlifetime will then use the maximum for that setting found in any of those files.

Editing maxlifetime won't help or at least only until the php5-common package is updated again.