The program cron is in local/program/cron.php.

Some resource intensive activities only run hourly or daily but that restriction can be changed by modifying these lines:

$hourlycron = 60 * 60; // one hour
$dailycron = 60 * 60 * 24; // one day

if you set them to zero the cron will run every time.

However, I don't think this would be the cause of your problems, because some messages are being sent - it seems more likely that an error is occuring part way through the sending, so some users get their messages but others don't.

Not sure why no errors are showing up though - do you have debugging turned on?

Simon