I believe we have discovered a bug in Moodle 2.9.1 that hasn't been fixed in the latest releases. I've added this to the tracker site too, but am posting here in case others have experienced the problem and need a work around. I didn't see it addressed in the 2.9.2 or .3 release notes, so I believe it is still a bug.
A professor using natural aggregation sees correct grades for students in grader and user reports.
The students see a different, incorrect grade, that includes empty grades (even though the settings are chosen to not include empty grades). In short, the student all see that they are failing, while the professor's view has correct grades.
If the professor has any item hidden in the grade book, including an un-closed quiz, that is triggering the student view of grade book to include ALL empty grades. If all hidden items are revealed or deleted from grade book, student grades recalculate to be correct.
In order to duplicate, you must be able to log in as a student (this ONLY shows up on student view - the prof and admins will see the grade as calculating correctly).
Our Moodle admin/programmer will be working on a patch and will post to the tracker site when one is developed, but we are a very small institution and it might be several weeks.
Here is the link to the tracker issue... https://tracker.moodle.org/browse/MDL-52078