Perhaps that's not really where the php.ini is located. Did you build PHP from scratch or use a binary installation. Sometimes you find the one its using in /etc or /usr/local/php or a million other places. Try doing a 'whereis php.ini' or 'slocate php.ini' and see if multiple copies are lying around.
Of couse, you could load this test file from a browser and it will tell you where the ini file is:
<?php phpinfo(); ?>