Assuming that one setting is the only one that is missing, then Gavin's mysql command should fix things. Note that you will have to run the command once for each affected course.
I believe that rather than listing the gateway sets, you could get away with the following command to fix all of the sets within the course:
mysql> update `[coursename]_set` set hide_score_by_problem='N' where hide_score_by_problem is null;
This will set "hide_score_by_problem" to no for any set where it is undefined.
I haven't tested this, so I recommend running it on a test course and checking that it doesn't break either a gateway quiz or a regular homework set before running it on your live courses.
I haven't tested this, so I recommend running it on a test course and checking that it doesn't break either a gateway quiz or a regular homework set before running it on your live courses.