*I'm working with Joe on the same moodle site fyi*
What's weird is that I will run the assignment upgrade tool and it will duplicate the issue assignment, but only the very first one in the queue. It will keep the old 2.2 assignment version but create a working duplicate. When I delete the 2.2 bad assignment it will remove it from being a trouble assignment. Then, i run the upgrade tool again and it duplicates the next one in the queue..I delete that one, keep the new one created...again and again.
So it seems like it creates a duplicate, working assignment but does not delete the bad version so I'm doing it manually.
Do you think that is a problem? (obviously the URL changes). Does that tell you anymore that would tell us what's going on here?