If you have no idea what "PHP_INI_PERDIR" or "PHP_INI_USER" are or how they relate to setting a .user.ini file, take a look at the ini.list page: http://www.php.net/manual/en/ini.list.php
Basically, anything in the "Changeable" column labeled as PHP_INI_SYSTEM can't be set in the .user.ini file (so quit trying). It can ONLY be set at the main php.ini level.
Since PHP 5.3.0, PHP includes support for .htaccess-style INI files on a per-directory basis. These files are processed only by the CGI/FastCGI SAPI. This functionality obsoletes the PECL htscanner extension. If you are using Apache, use .htaccess files for the same effect.
In addition to the main php.ini file, PHP scans for INI files in each directory, starting with the directory of the requested PHP file, and working its way up to the current document root (as set in $_SERVER['DOCUMENT_ROOT']). In case the PHP file is outside the document root, only its directory is scanned.
Only INI settings with the
PHP_INI_USER will be recognized in .user.ini-style INI
Two new INI directives, user_ini.filename and user_ini.cache_ttl control the use of user INI files.
user_ini.filename sets the name of the file PHP looks for in each directory; if set to an empty string, PHP doesn't scan at all. The default is .user.ini.
user_ini.cache_ttl controls how often user INI files are re-read. The default is 300 seconds (5 minutes).
This article should be made clearer.
".htaccess-style INI files" meant to me that the ini settings had to follow the syntax used in .htaccess, but this is not the case!
You have to use
php_flag register_globals on
Also, the changes can take a while to propagate to all processes if you have a long process time out.
Restarting php-fpm can give you an answer quicker :)
Currently .user.ini files aren't read when using php-fpm, instead you can use [HOST] and [PATH] sections in your main php.ini to set per directory and per domain settings: http://us3.php.net/manual/en/ini.sections.php
As of PHP 5..3.6, applicable .user.ini files are *not* listed or identified in phpinfo() output.
A .user.ini file can be in effect even when phpinfo() shows "additional .ini files parsed: (none)"