Comment 13 for bug 759898

I notice that Thunderbird does not integrate properly with the Unity menus, in that it always shows its own menubar within its application window.

It sounds like what is going on is because Thunderbird is starting before the window manager, it uses the full screen geometry from X. Because it's not interacting properly with the window manager (as evidenced the lack of menu integration) it does not adjust itself properly to the new geometry available once the window manager has started.

Just a theory.