Plesk 12.x / Linux :: Wordpress Toolkit Complaining That PHP Version Is Not 5.3 Or Higher

We are trying to use the new Wordpress toolkit, but when we try to install an instance it says this:

Contact your service provider for assistance. Upgrade the system PHP CLI to version 5.3.0 or later, or set the correct path to the PHP CLI in the clipath option of the php_handler utility for a custom PHP handler.

Screenshot:

Now that would not be a problem if the requirements were not met, but there are installed PHP versions that are higher than 5.3 and the website is configured to us these versions...

# /usr/local/psa/bin/php_handler --list
id: display name: full version: version: type: cgi-bin: php-cli: php.ini: custom:
2 5.5.14 5.5.14 5.5 fastcgi /usr/local/php5514-cgi/bin/php-cgi /usr/local/php5514-cgi/bin/php /usr/local/php5514-cgi/etc/php.ini true
3 5.3.29 5.3.29 5.3 fastcgi /usr/local/php5329-cgi/bin/php-cgi /usr/local/php5329-cgi/bin/php /usr/local/php5329-cgi/etc/php.ini true
cgi 5.2.17 5.2.17 5 cgi /usr/bin/php-cgi /etc/php.ini false
fastcgi 5.2.17 5.2.17 5 fastcgi /usr/bin/php-cgi /etc/php.ini false
module 5.2.17 5.2.17 5 module /usr/bin/php-cgi /etc/php.ini false

The website is using this version, and the PHP CLI is defined in the php_handler tool

I must be missing something obvious.