Problem solved! I posted to Thomson's email discussion list, and John East of the University of Queensland Library replied with a solution. There are tags within the filter that EndNote uses to decide which filter to choose to import the references. There was another filter with the same settings for those tags, and EndNote was using that filter instead. That filter (the one for Ovid AutoAlerts) was set to import AU and FA both into the Author field.
I would never have thought of this in a long time! Most grateful to John for his help.