I had same issue with that one too.
I modified it a bit, and took out the WHERE clause, but don't have enough real certificates to test thoroughly; worked okay on my sample data. It is much simpler (uglier) version that yours.
SELECT u.username, c.shortname, t.name, l.timecreated
FROM prefix_certificate_issues l
JOIN prefix_user u ON l.userid = u.id
JOIN prefix_certificate t ON l.certificateid = t.id
JOIN prefix_course c ON t.course = c.id
ORDER BY u.username, c.shortname
This works on the Simple Certificate module as well, if you just change the table names to _simplecertificate and _simplecertificate_issues. Same field names mostly.
- Randy