~~It seems like the module currently completely ignores (doesn't compare) the cron last execution time and the set frequency that it should be executed and just follows the run frequency set in the server cron manager.
That said,~~ to fix the time not getting updated, do this:
Edit /modules/cronjobs/controllers/front/cron.php
Find:
'updated_at' => ['type' => 'sql', 'value' => 'IF (`one_shot` = TRUE, FALSE, `active`)'],
Replace with:
'updated_at' => ['type' => 'sql', 'value' => 'NOW()'],
'active' => ['type' => 'sql', 'value' => 'IF(`one_shot` = TRUE, FALSE, `active`)'],
Hope this helps :)