Your PHP setup should only load a single ini file for the settings. It will look in the C:\windows directory and your local install directory for php. If you create a phpinfo page it will show you which ini file is loaded. An info page is any php page that has this code in it:
<?php phpinfo(); ?>
If you don't have one already create a new page and have just this in it. You should be able to see the setup info for your php including the loaded ini file. If you cannot view the page then this would indicate that there is an issue with your server setup in IIS. If you do get an error here post back with the exact error message text if you need help with it.