php.ini in cgi vs php.ini in cli

In the php configurations directories /etc/php5, there are 2 subdirectories, one for cgi and one for cli. There is a php.ini file in each of these directories. What would cause a difference of behavior in these 2 environments with the php.ini exactly the same in each directory?? I have a command line script that consequently uses the cli version. This script works just fine in that it can access API function in modules that are loaded via cli/php.ini However, when executing in the cgi environment, I get a "call to undefined function" error even though my 2 php.ini files are exactly the same. Any idea what is causing this? thanks, -Andres