Hi guys, I have the same problem.
In my case, in order to have the certificate, participants must have finished two assignments. As tutors have entered their scores directly into the gradebook, their certificates are not being printed.
This is because the certificate module seeks the score in each activity table, not in the gradebook.
This other issue has more details of how to solve it:
There is an open issue in Moodle's JIRA: http://server3.moodle.com/browse/CONTRIB-2760 but, unfortunately, there is no patch available yet.