Did you run 'sh /script/fixweb; sh /script/restart-web' after 'yum replace'?.
Inform here 'yum list installed php* mysql*'.
yum list installed php* mysql*
Loaded plugins: fastestmirror, priorities, protectbase, replace
Loading mirror speeds from cached hostfile
* base: mirror.net.cen.ct.gov
* epel: mirror.metrocast.net
* extras: mirror.rackspace.com
* mratwork-epel: mirror.metrocast.net
* mratwork-ius-stable: ius.mirror.constant.com
* remi-php55: remi.check-update.co.uk
* remi-safe: remi.check-update.co.uk
* updates: mirror.net.cen.ct.gov
0 packages excluded due to repository protections
Installed Packages
mysql55.x86_64 5.5.45-1.ius.el6 @mratwork-ius-stable
mysql55-libs.x86_64 5.5.45-1.ius.el6 @mratwork-ius-stable
mysql55-server.x86_64 5.5.45-1.ius.el6 @mratwork-ius-stable
mysqlclient16.x86_64 5.1.61-4.ius.el6 @mratwork-ius-stable
php52s.x86_64 5.2.17-12.mr.el5 @mratwork-release-version-arch
php53u.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-bcmath.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-cli.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-common.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-fpm.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-gd.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-mbstring.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-mcrypt.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-mysql.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-pdo.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-pear.noarch 1:1.9.4-3.ius.el6 @mratwork-ius-archive
php53u-pecl-geoip.x86_64 1.0.8-1.ius.el6 @mratwork-ius-archive
php53u-pgsql.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive
php53u-xml.x86_64 5.3.29-1.ius.el6 @mratwork-ius-archive