This is the same issue as MDL-21449, which was closed for inactivity. If you create the a grade category with the aggregation method "Simple weighted mean of grades" and add items to it those items do not have the extra credit box checked by default. However, if you change the aggregation method for a category to "Simple weighted mean of grades" then all the items in that category will have the extra credit box checked.

Steps to reproduce:

1. Create a gradebook category with the aggregation method "Weighted mean of grades."
2. Add some items to the category, without the extra credit box checked.
3. Change the aggregation method on that category to "Simple weighted mean of grades."