I am having a very similar problem in Moodle 2.0.
1. When students left a lesson early, it consistently returned them to the first page of the lesson, even though they wanted to see the last page they had seen AND had entered correct answers. I tested this myself. They lost all of their work every time unless they worked through to completion.
2. In grading, even though the lesson has several ungraded essays, it shows that everyone has 100%. It saved my comments but not the score. When I go back in, it shows as 0.
3. In 1.9, when i graded an essay it would turn from red to green in the list, this doesn't show any difference.
I have it set as a grade of 20, custom scoring, not a practice lesson, no student review, no retakes. I've played with other settings, allowing student review, allowing progress bar,e tc, but nothing made a difference when i tested it with my student account.