As my latest experiment with the disappearing virt-manager windows, I was able to bring them up as long as I tell fvwm they should be unmanaged.
Once the window exists, I can edit the fvwm config file, remove the style that says unmanaged, and restart fvwm and the windows get decorations and operate perfectly normally (until I want to popup a new one, of course). So obviously what I need is a new UnmanageWithTimeout style that waits a specified number of milliseconds before trying to manage the window :-).