php.ini in cgi vs php.ini in cli

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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

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