I have some issues with the native mail app too and have to use K-9 Mail 
Anyway, I found this bug report which gives some hints.
In my opinion, a crappy workaround to solve it is to restart messageserver5 as a normal user:
systemctl --user restart messageserver5
Of course, some logs would be useful to fix this issue. Have a look at this tutorial to collect logs related to the email app. If you need help, don’t hesitate to send me a private message.