It's not always easy, in PHP, to figure-out which PHP ini files are actually parsed and loaded. CLI may use diff set than web, and if you are using NginX with FPM, there may be yet another set.

Following extremely simple piece of code can greatly help to clear-up the confusion:

print_r( php_ini_loaded_file() );
print_r("Scanned: ");
print_r( php_ini_scanned_files() );