Add a wrapper into the master configuration.php file to route on the appropriate configuration.php file when an extension want include the Joomla configuration file from a slave site.

This problem was detected with VirtueMart PayPal notify.php script that was using the master Joomla Configuration file instead of a Slave site one.
This was due to the fact that this PayPal notify script is not called trough the index.php file.
This is a standalone script.