Sorry, JRWhy, can't offer any advice but can add to the Mail fails that my MBP has been experiencing since the 'upgrade' to El Capitan.
Emails vanish from the screen while I'm reading. They can be recovered by clicking on them again in the Mail list window. Their disappearance doesn't coincide with a new email's arrival, as queried by a forum member.
Resetting Mail Preferences to 'Show most recent at the top' has no effect. The oldest emails are always at the top when I open Mail, meaning I have to scroll through all the saved emails to the end to see the new emails.
I know that's not your specific problem but the whole cluster of fails might suggest something to the experts.
Mavericks was the last update that worked well for me.
Edit: 2. has been solved, thank you....didn't know to toggle the 'Date received' header.