Well admin/cron.php basically calls every single components own cron function (if it exists). The Program cron does most of the calculations daily. In the normal course of events when people are using the system day-to-day there is instant course completion which would normally trigger Program completion too, but I'm not sure if that works properly when using the course completion import tool.

There are a few outstanding enhancement requests to improve Programs and yeah it would be best if they always completed instantly in all circumstances.

In the meantime if you want you could

DELETE FROM mdl_config WHERE name='totara_program_lastdailycron';

Then just run admin/cron.php and that should make the full program cron stuff run every time, which may be useful for testing but not really recommended once the site is in production :-)