Hi Daniel,
In my experience the Weighted mean works with whatever the item score or category total is so shouldn't matter how that score is achieved. I havn't tested it with the extra credit though.
You can read the details of Weighted mean calculations and the others in the docs here:
http://docs.moodle.org/23/en/Category_aggregation#Weighted_mean
Mal.
Gradebook
Weighted mean of grades and sum of grades
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