Currently there is no logic behind what email address field is used for deciding which Contact to associate an email with. If you have custom email column that is storing an email address, it is possible for it to be "found" as the Contact sending an email, even if that email exists in a different Contact's "emailaddress" column. It would be better if there was a documented precedence of email columns that are searched for matching that could be controlled by a system administrator. For example, I would prefer it to ALWAYS match to the Contact where the given email address exists in the "emailaddress" column, follow by "emailaddress2", "emailaddress3", then any custom email columns in the Contact table.