If you install fusion icon from the repositories then you can toggle your
window managers and decorators. It sits in the system tray and allows you to
switch as you want. That way you can switch between metacity and compiz and
emerald and gtk --- just in case things mess up.

As for your problem, I am not sure what is happening with emerald. It does
not seem to be under development as Compiz Fusion is working to replace it
as a decorator. I would probably look at using a different decorator in the
mean time. There are many Gnome GTK themes that you can get from
Gnome-look.org.

http://wiki.compiz.org/CompizFusionIcon

I am assuming that Compiz is otherwise working well. If not, then that could
be the source of your problem as Emerald works with Compiz.