Your post suggests that you have referenced the Loader in two php.ini files, the main php.ini and a second one (ioncube.ini) located in an additional ini scan directory. The ionCube Loader must be installed only once, and ideally referenced in only one php.ini file.
Produce phpinfo() output from both the webserver and CLI PHP used by the cron job, and check to see if the referenced php.ini locations are the same. Also check that the PHP version is the same as sometimes it isn't due to PHP being updated incorrectly/incompletely on a server.
If the PHP version is the same and there is a common php.ini file being referenced, such as /usr/local/lib/php.ini, then that's the best place to place the zend_extension line for ionCube. You can use -c to specify the location of a php.ini file if needed.
If the PHP version is different, you must not use the same php.ini file that references the Loader as you need different Loaders. Use a different php.ini file for the CLI case and reference its location with -c. Consider fixing the installation to use the same PHP version for web and CLI though.
Probably not the case here, but if you have edited only one php.ini file to reference the Loader, it would suggest that the php.ini file is being read twice. This is a flaw in PHP and can happen if the main php.ini directory is also one of the additional scan directories.