You do not need to put anthing to do with PHP anywhere near the c:\windows
folder.
If you do it will only serve to mess you up when you upgrade PHP to a new version.
If you CD to the folder that PHP is installed in and do a php --ini
it will read the php.ini file from the folder that you are in.
D:\wamp\bin\php\php5.5.12>php --ini
Configuration File (php.ini) Path: C:\Windows
Loaded Configuration File: D:\wamp\bin\php\php5.5.12\php.ini
Scan for additional .ini files in: (none)
Additional .ini files parsed: (none)
I think its also a bad idea to put the PHP install folder in the windows PATH as well.
All you need is a little batch file that will setup your PATH for the duration of the command window you are using, and put that in one of the folders that is already in the windows PATH.
So assuming you installed PHP into C:\php
this is the batch file
phppath.cmd
PATH=%PATH%;C:\php
php --ini
php -v
And you then just run this batch file any time you open a command windows and want to run some PHP code and your environment gets configured. You can also add other things to this batch file when you need other things added to your environment like Composer etc.