I just quickly set up a lesson in Moodle 1.9 and tried it out as a student. My lesson has three questions. I answered 2 of them incorrectly the first time, then correctly the second time. My student account got 100% (3/3) on the lesson.
So, a few settings to check:
Make sure practice lesson is set to "no" - this probably isn't your problem, as I assume the lesson is showing up fine in your gradebook.
Custom scoring is set to "yes". Then for each question, make sure the correct answer gets assigned a positive number, and the incorrect answer(s) are assigned 0 as their grade. Again, this hasn't changed at any point and is probably not your problem, but worth checking.
Make sure the maximum grade achievable reflects the maximum grade of all the questions. Mine had three questions, each worth 1 point.
Handling of retakes is set to "Use maximum". This ensures that their maximum grade is the one taken.
Are these settings all correct? If they are, I can keep looking for you.