See the attached glass.java. Basically, it emulates the behavior of FX menu items added to a popup menu in the onMenuShowing() handler in pre- RT-35401 world.
The menu items would first fire the user event handler, and only then proceed with closing the menu. If the user event handler opens another window, then a number of requestFocus() calls are performed that result in some wild focus swings. In the end, however, the focus gets to the secondary window from Glass/FX perspective. From native perspective the focus also gets to the secondary window on all the platforms but Mac.

On Mac, after processing all the wild focus requests mentioned above, the OS considers the main window being focused. Note that the focus events that we receive from the native system regarding focus changes are exactly the same on all platforms, and so Glass/FX rightfully consider the secondary window being focused.