gconftool-2 -s '/apps/metacity/general/compositing_manager' --type bool true
Enable Metacity Compositing in GNOME 2.22 | Tombuntu

Do this:
Create /usr/share/applications/compiz.desktop containing the following:
Code:
[Desktop Entry]
Type=Application
Encoding=UTF-8
Name=Compiz
Exec=compiz ccp
NoDisplay=true
# name of loadable control center module
X-GNOME-WMSettingsModule=compiz
# name we put on the WM spec check window
X-GNOME-WMName=Compiz
Load gconf-editor then browse within it to /desktop/gnome/session/required_components/ and change the windowmanager entry to compiz
Logout, log back in and that should fix it (it did for me) Provided of course that you have selected Emerald through the Fusion Icon at some point?
Arch Linux Forums / Novice in ArchLinux – Problems with Compiz-Fusion in Gnome.

((type=Menu | PopupMenu | DropdownMenu | Tooltip | Notification | Combo | Dnd | name=sun-awt-X11-XWindowPeer)) & !(name=sun-awt-X11-XFramePeer | name=sun-awt-X11-XDialogPeer)
http://www.ubuntu1501.com/2007/12/transparencies-and-opacity-in-compiz.html