What is happening is this. When you click the option to install install PHP 5.2 (Single php.ini) with IonCube, that adds php handler/php.ini handler .htaccess code in your root .htaccess file. So what you need to do is click the option again to install PHP 5.2 (Single php.ini) with IonCube and then copy that php handler/php.ini handler .htaccess code that is added in your root .htaccess file into this BPS Custom Code text box: to save it permanently.
You can then do the rest of the Root Custom Code steps.
Click the Save Root Custom Code button.
Go to the Security Modes page, click the Create secure.htaccess File AutoMagic button and activate Root folder BulletProof Mode.