I don't have an explanation for the second grade item, yet. I would be interested to see a screenshot of the categories and items page as well as the settings for the course category in order to investigate further. Do you have the course category in the gradebook set to drop any scores?
Also, what version of moodle is this running? Worth noting if this is all tied to a bug in a particular version - although I'm not aware of any grade calculation bugs off the top of my head.