Never had this problem till updated CPanel today? Maybe that is part the problem?

I only have the one php.ini file

# /usr/local/bin/php --info | grep php.ini
Configure Command =>  './configure'  '--disable-cgi' '--disable-fileinfo' '--enable-bcmath' '--enable-calendar' '--enable-exif' '--enable-ftp' '--enable-gd-native-ttf' '--enable-libxml' '--enable-magic-quotes' '--enable-mbstring' '--enable-pdo=shared' '--enable-soap' '--enable-sockets' '--enable-zip' '--prefix=/usr/local' '--with-bz2' '--with-config-file-path=/usr/local/lib' '--with-config-file-scan-dir=/usr/local/lib/php.ini.d' '--with-curl=/opt/curlssl/' '--with-curlwrappers' '--with-freetype-dir=/usr' '--with-gd' '--with-imap=/opt/php_with_imap_client/' '--with-imap-ssl=/usr' '--with-jpeg-dir=/usr' '--with-kerberos' '--with-libdir=lib64' '--with-libexpat-dir=/usr' '--with-libxml-dir=/opt/xml2' '--with-libxml-dir=/opt/xml2/' '--with-mcrypt=/opt/libmcrypt/' '--with-mysql=/usr' '--with-mysql-sock=/var/lib/mysql/mysql.sock' '--with-mysqli=/usr/bin/mysql_config' '--with-openssl=/usr' '--with-openssl-dir=/usr' '--with-pcre-regex=/opt/pcre' '--with-pdo-mysql=shared' '--with-pdo-sqlite=shared' '--with-pic' '--with-png-dir=/usr' '--with-pspell' '--with-sqlite=shared' '--with-tidy=/opt/tidy/' '--with-xmlrpc' '--with-xpm-dir=/usr' '--with-xsl=/opt/xslt/' '--with-zlib' '--with-zlib-dir=/usr' '--with-gettext'
Configuration File (php.ini) Path => /usr/local/lib
Loaded Configuration File => /usr/local/lib/php.ini
Scan this dir for additional .ini files => /usr/local/lib/php.ini.d

# /usr/bin/php --info | grep php.ini
<tr><td class="e">Configure Command </td><td class="v"> &#039;./configure&#039;  &#039;--disable-fileinfo&#039; &#039;--enable-bcmath&#039; &#039;--enable-calendar&#039; &#039;--enable-exif&#039; &#039;--enable-ftp&#039; &#039;--enable-gd-native-ttf&#039; &#039;--enable-libxml&#039; &#039;--enable-magic-quotes&#039; &#039;--enable-mbstring&#039; &#039;--enable-pdo=shared&#039; &#039;--enable-soap&#039; &#039;--enable-sockets&#039; &#039;--enable-zip&#039; &#039;--prefix=/usr&#039; &#039;--with-bz2&#039; &#039;--with-config-file-path=/usr/local/lib&#039; &#039;--with-config-file-scan-dir=/usr/local/lib/php.ini.d&#039; &#039;--with-curl=/opt/curlssl/&#039; &#039;--with-curlwrappers&#039; &#039;--with-freetype-dir=/usr&#039; &#039;--with-gd&#039; &#039;--with-imap=/opt/php_with_imap_client/&#039; &#039;--with-imap-ssl=/usr&#039; &#039;--with-jpeg-dir=/usr&#039; &#039;--with-kerberos&#039; &#039;--with-libdir=lib64&#039; &#039;--with-libexpat-dir=/usr&#039; &#039;--with-libxml-dir=/opt/xml2&#039; &#039;--with-libxml-dir=/opt/xml2/&#039; &#039;--with-mcrypt=/opt/libmcrypt/&#039; &#039;--with-mysql=/usr&#039; &#039;--with-mysql-sock=/var/lib/mysql/mysql.sock&#039; &#039;--with-mysqli=/usr/bin/mysql_config&#039; &#039;--with-openssl=/usr&#039; &#039;--with-openssl-dir=/usr&#039; &#039;--with-pcre-regex=/opt/pcre&#039; &#039;--with-pdo-mysql=shared&#039; &#039;--with-pdo-sqlite=shared&#039; &#039;--with-pic&#039; &#039;--with-png-dir=/usr&#039; &#039;--with-pspell&#039; &#039;--with-sqlite=shared&#039; &#039;--with-tidy=/opt/tidy/&#039; &#039;--with-xmlrpc&#039; &#039;--with-xpm-dir=/usr&#039; &#039;--with-xsl=/opt/xslt/&#039; &#039;--with-zlib&#039; &#039;--with-zlib-dir=/usr&#039; </td></tr>
<tr><td class="e">Configuration File (php.ini) Path </td><td class="v">/usr/local/lib </td></tr>
<tr><td class="e">Loaded Configuration File </td><td class="v">/usr/local/lib/php.ini </td></tr>
<tr><td class="e">Scan this dir for additional .ini files </td><td class="v">/usr/local/lib/php.ini.d </td></tr>

everytime I restart apache I still seem to be running the old one. Nothing changes.

I removed phpinfo() and ini_set() from the php.ini but I still can't use them.

# service httpd -k restart
[Fri Oct 26 15:27:10 2012] [warn] module hostinglimits_module is already loaded, skipping
[Fri Oct 26 15:27:10 2012] [warn] NameVirtualHost 127.0.0.1:8081 has no VirtualHosts

There is also no php.ini files under the vhosts or .htaccess.

# /usr/bin/php -v
PHP 5.3.15 (cgi-fcgi) (built: Aug  4 2012 21:33:58)
Copyright (c) 1997-2012 The PHP Group
Zend Engine v2.3.0, Copyright (c) 1998-2012 Zend Technologies
    with eAccelerator v0.9.6.1, Copyright (c) 2004-2010 eAccelerator, by eAccelerator
    with the ionCube PHP Loader v4.2.2, Copyright (c) 2002-2012, by ionCube Ltd., and
    with Zend Guard Loader v3.3, Copyright (c) 1998-2010, by Zend Technologies
    with Suhosin v0.9.33, Copyright (c) 2007-2012, by SektionEins GmbH

and

# /usr/local/bin/php -v
PHP 5.3.15 (cli) (built: Aug  4 2012 21:34:27)
Copyright (c) 1997-2012 The PHP Group
Zend Engine v2.3.0, Copyright (c) 1998-2012 Zend Technologies
    with eAccelerator v0.9.6.1, Copyright (c) 2004-2010 eAccelerator, by eAccelerator
    with the ionCube PHP Loader v4.2.2, Copyright (c) 2002-2012, by ionCube Ltd., and
    with Zend Guard Loader v3.3, Copyright (c) 1998-2010, by Zend Technologies
    with Suhosin v0.9.33, Copyright (c) 2007-2012, by SektionEins GmbH

Nothing shows up in the error logs either. The only errors we get are under the vhost's with error_log saying phpinfo and ini_set are disabled.

EDIT: Both php binaries use the same php.ini file

EDIT: Running php as mod_fgcid.so with suexec

EDIT: From SSH I see the correct values for PHP from the php.ini file being loaded from both binaries

When using php from apache [26-Oct-2012 20:25:34 UTC] PHP Warning: phpinfo() has been disabled for security reasons in /home/jake/public_html/phpinfo.php on line 1

EDIT: /usr/bin/php is the correct PHP file. Forgot to mention. It is the one in the wrapper script.