It seems like bluefish is creating two GtkMenuBar widgets in its main application window. Those are removed by the menuproxy gtk module. Indicator-appmenu only displays the menu bar for the currently active toplevel window, it doesn't have a concept of subwindows which can be "active". I'm pretty sure that this would require some work in GTK to get done.
(In reality though, creating two GtkMenuBar widgets seems like a bit of an odd application design choice then)
This isn't a compiz bug.
It seems like bluefish is creating two GtkMenuBar widgets in its main application window. Those are removed by the menuproxy gtk module. Indicator-appmenu only displays the menu bar for the currently active toplevel window, it doesn't have a concept of subwindows which can be "active". I'm pretty sure that this would require some work in GTK to get done.
(In reality though, creating two GtkMenuBar widgets seems like a bit of an odd application design choice then)