Well, I must say you certainly piqued my curiosity. Just for giggles, I loaded a fresh snapshot of 5.7 with the default httpd, MySQL (5.0) and PHP (5.1) configurations, and then installed virtualmin/webmin. I plopped a phpinfo file in the /html directory and it worked as expected. Next I activated the Atomic repo and ran a yum upgrade. This bumped my versions of MySQL and PHP to 5.5.18 and 5.3.8 respectively. I think this is probably what has been done on your server as well. I did a quick "service httpd restart" and then rechecked the phpinfo file. Still working as expected. The output of "rpm -qa | grep php" on my server is now almost identical to yours, with the exception of having no duplicate entries. I honestly don't know if that is a significant clue or not.
I think at this point, if everything in /etc/httpd/conf.d/php.conf looks okay, you may want to put in a service call to your host as ChristiNi suggested. As slow as that might seem to be, they might be able to quickly point you to a solution. I'm sorry I couldn't duplicate the issue and offer a solution, but I had fun trying!
 your php.conf is identical to mine.