I had a client who needed CubeCart installed on a Dreamhost site. The installation seemed easy enough, but then I ran into the following error message:
Site error: the file /home/username/domain.com/index_enc_ion.php requires the ionCube PHP Loader ioncube_loader_lin_5.2.so to be installed by the site administrator.
This site was using a custom php.ini file (see http://wiki.dreamhost.com/Php.ini#Custom_php.ini_for_a_Single_domain for more info on setting up a custom php.ini file on Dreamhost).
I double-checked, and ion loader was in the webroot, and it had the correct line in the php.ini file. (Important to note that the ion loader line in the php.ini file must be before any of the Zend extension lines). After some investigating, I discovered that this could be fixed by opening up a shell command line and running:
[server]$ killall -9 php5.cgi
[server]$ touch /home/username/domain.com/cgi-bin/php-wrapper.fcgi
This reset things and allowed ion loader to install correctly. After this, the install worked fine.