Mail not seeing new mail with smtp settings. I am having to quit and restart Mail for it to see new mail.

Mail not seeing new mail with smtp settings. I am having to quit and restart Mail for it to see new mail. Also, mail will arrive in my inbox and disappear before I can open it. I am connecting to a godaddy email account through mail. godaddy claims it has something to do with El Capitan. Has anyone had this same problem and fixed it?