In-Portal uses output compression (used for the web) to speed up page loading. Internally PHP output buffering is used for that.
The same output buffering is also enabled for CLI operations (e.g. /tools/cron.php and /tools/run_event.php script). As a result, their output is shown only after the script has finished executing and not in real-time.
Solution
Place define('SKIP_OUT_COMPRESSION', 1); code before application initialization in /tools/cron.php and /tools/run_event.php scripts.