This took me a few hours to solve so I hope it helps someone else. My gotcha was one of the addition PHP ini files was loading an old version of ioncube. It was simple looking back...
If you are installing Ioncube Loader on Virtual Private Server with Plesk checkout http://blog.ucvhost.com/?p=126
Get correct ioncube version from http://www.ioncube.com/loaders.php
If you are getting Permission denied checkout here http://firelinux.wordpress.com/2009/08/25/selinux-problem-in-ioncube-installation/
If you have done everything correctly and php -v returns something like: Failed loading /usr/lib/php/modules//php_ioncube_loader_lin_5.1.so: /usr/lib/php/modules//php_ioncube_loader_lin_5.1.so: undefined symbol: zend_unmangle_property_name_ex
Load phpinfo.php and run it
Look for "Scan this dir for additional .ini files" it maybe show something like /etc/php.d
Check this directory for something like /etc/php.d/ioncube-loader.ini
If found then you can remove the entry from /etc/php.ini
Now double check what package and directory ioncube-loader.ini is referencing - in my case it was wrong. Fix the package and directory reference
Restart Apache /etc/init.d/httpd restart
Check php -v