Comment 7 for bug 990689

That configuration file reports that you actually changed two options. Can you please delete that file ("rm ~/.config/unity-mail.conf"), relogin and check if the issue still exists?

Also, do you use regular Unity or Unity 2D? Are you sure you have the latest unity-mail ("apt-cache policy unity-mail" should say 0.92.2)?

You also say that "messages appear twice". Does *every* message appear twice? Can you please provide a screenshot? (You can use "gnome-screenshot -i -d 10" to take a screenshot of messaging menu).

I really can't find anything this issue may be caused by…