It seems that the top bar menus grab focus when they are opened, and release it when they are closed. This means that when you open a menu and you move the pointer over another menu to open it, the currently focused application gets the focus for one instant, and loses it immediately in favor of the newly-opened menu. Instead of this weird behavior, the Shell should keep the focus when it knows a menu is closed because another is being opened.

This bug can be checked for example using Firefox: go to any webpage, clar the contents of the address bar, and play with the Shell's menus. You'll notice grey text appears and disappears in the address bar when you move to a new menu. Any window which has a focused widget (e.g. Evolution's tree view) will also trigger the same graphical weirdness, but depending on the GTK theme it is often harder to notice.