Modal windows

I am developing a system which implements modal ‘popups’ using the technique I previously mentioned in this thread. However, I am now using an interface with a navigation bar docked north, with the main window filling the rest of the screen.

When I open the popup, it only covers the main part of the window, meaning that the user can still press buttons on the buttonbar. Is there any way to force the popup to occupy the whole screen even if there are docked windows present? I tried changing the window layer, but without success.