Quite likely the server php.ini included Ioncube support directly. I'll bet the custom php.ini that you added, *didn't* include the Ioncube loader, which is why you saw that error.
You can download the Ioncube loader files from
http://www.ioncube.com, to find out. Just put the /ioncube/ folder in the root of your X-Cart installation, if it works (while that custom php.ini is in place), then you won't have to worry about it any further
