Procedure
Instead of using --cleandupes use the following that will take the list of RPMs and then clear the RPM from the RPM database and then reinstall that RPM to ensure it is fully installed.
package-cleanup --dupes | tail -n +3 | sort --version-sort | awk 'NR % 2 {print "rpm -e --justdb --nodeps " $1 } !(NR % 2) {match($0, "-[0-9]");print "yum -y reinstall " substr($0,0,RSTART-1)}' | sh
