Description:
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Installed php-5.2.14-Win32.zip with Apache 2.2.16. Noticed that php.ini was not being read. Though running phpinfo() showed:
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Configuration File (php.ini) Path  C:\WINDOWS  
Loaded Configuration File  D:\Php\php.ini  
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Interestingly, even if I delete/rename the pointed php.ini, Apache still restarts fine without any error & my phpinfo shows:
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Configuration File (php.ini) Path  C:\WINDOWS  
Loaded Configuration File  
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Though, there is no php.ini at C:\Windows.

Even when I tried putting just one (& only one) php,ini at C:\Windows, it was still not reading the php.ini (e.g. my changes to add/remove any extension was not reflecting).

My Apache httpd.config reads like:
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LoadModule php5_module "D:/Php/php5apache2_2.dll"

<IfModule php5_module>
PHPIniDir "D:/Php/php.ini"
   <Location />
	AddType application/x-httpd-php .php
	AddType application/x-httpd-php-source .phps

	AddType text/html .php .phps
	AddHandler application/x-httpd-php .php
	AddHandler application/x-httpd-php-source .phps   
   </Location>

</IfModule>
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When I removed php-5.2.14 by freshly downloaded php-5.3.3-Win32-VC9-x86.zip content, it started to work per expectation i.e. php.ini was correctly evaluated/read.

Expected result:
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php.ini should be evaluated/read

Actual result:
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php.ini was not being evaluated/read