Según la documentación oficial de PHP:
Cita: By default on UNIX it should be in /usr/local/lib which is <install-path>/lib. Most people will want to change this at compile-time with the --with-config-file-path flag. You would, for example, set it with something like:
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--with-config-file-path=/etc
And then you would copy php.ini-dist from the distribution to /etc/php.ini and edit it to make any local changes you want.
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--with-config-file-scan-dir=PATH
On Windows the default path for the php.ini file is the Windows directory. If you're using the Apache webserver, php.ini is first searched in the Apaches install directory, e.g. c:\program files\apache group\apache. This way you can have different php.ini files for different versions of Apache on the same machine.
See also the chapter about the configuration file.
Al parecer nunca movistes ese php.ini-dist (y cambiar la extensión a sólo php.inio) al directorio indicado (y que tienes que indicarlo con la directiva de compilación que se menciona).
Ref.:
http://www.php.net/manual/en/faq.installation.php
Un saludo,