This issue was identified by Steve Mattingly, a professor at LAMP Consortium member Davis & Elkins College. To recreate the problem, do the following:
0. Go to Gradebook -> Settings -> Grade Entry and set to Percentages.
1. Create a Gradebook item with Relative Weight of (say) 50. (To do this, Gradebook must be set to do Grade Entry with Percentages).
2. Create an Assignment with points scoring, and a maximum score that is different from the Relative Weight above-- say 200. Link this Assignment to the pre-existing Gradebook item.
3. In the Assignments tool, enter a score for some student on this Assignment-- say 40. (It isn't actually necessary for the student to submit anything). Save and release the grade.
4. The score that was entered is not the value that is saved. It is immediately and silently altered to x, where x (InstructorEnteredPoints / GradebookItemRelativeWeight) * 100. For specific numbers cited, the 40 entered is stored as x = 80, because 80 = (40 / 50) * 100. The associated Gradebook item shows a score of 80%.
As a contrast, Steve tried the same thing with Gradebook set to use Points, not Percentages, for Grade Entry. In that case, the 40 points entered is stored and displayed as 40, both on the Assignment and in the Gradebook. But this is misleading. From the Instructor's data entry, the score was 40 out of a maximum 200. But the Gradebook is recording it as 40 out of 50 points, and calculating the grade accordingly.
It's not clear how all this should work, but Steve feels (and I agree) that this isn't quite right. As Steve says, "I don't expect software to save a different number than the one I entered, at least not without some prominent warning and explanation."
(This issue was discovered on our production instance running Sakai 11.2. We're unclear if it applies to other versions.)