Hi Jozef,
The cron jobs are managed by WordPress, the plugin only registers the cronjob itself, and the period when to run. These are not the classical server triggered cron jobs though. It only works when a page is opened, so that PHP is triggered, and WordPress is initialized. It checks if there are any cron jobs due, then executes them. Therefore it is not possible to have this server controlled.
Maybe as a bypass solution you could set up a server cron job, that simply opens the site front-page, thus triggering WordPress to load. Setting it to maybe 5 minutes or so would trigger every remaining cron job.