The approach that is working well is to criple the Flash application's ability to determine the active window. If the application can't detect an active window change then it won't leave fullscreen mode.
This is done by a single byte edit of the Flash program file.
Using a binary or hex file editor (like "hexedit"), open libflashplayer.so. On my Ubuntu system, the command is:
sudo hexedit /usr/lib/flashplugin-installer/libflashplayer.so