RESOLUTION
In case there are other applications using Ioncube installed, the situation is possible when a conflict arises between the Ioncube installed by these applications and SiteBuilder. In this case one needs to find all occurences of Ioncube loader included in the PHP configuration files and leave only one line with the Ioncube included. The line looks like this:
zend_extension=/path_to/ioncube_loader_xxx_.x.x.so