When grades are entered manually via the gradebook or by file upload, there are no grades created for the specific activity (they are only stored in the mdl_grade_items table.) As a result, these are not viewed as valid grade submissions from the standpoint of the activity, and the certificate is not available to the student, even though the activity grading screen does show a grade has been assigned. Requesting that the certificate module be modified to look at the gradebook, as it is a more definitive source for information on activity grades.