Just a wild guess, but that can happen if you have miss-matched versions of compiz and emerald. Did you install everything from the fedora repository?
On my system (which works) I have:
$ rpm -q emerald compiz compiz-fusion
When you execute emerald --replace, do you get any output on the console? Do you get any error messages when you start compiz from the console? What hardware are you using? Have you set up your xorg.conf correctly? etc etc...
Try removing everything compiz related and reinstalling from the fedora repository.