The version of compiz-manager in Fedora uses the desktop dependent window
decorator by default (gtk-window-decorator/kde-window-decorator/kde4-window-decorator).
The upstream default configuration is to use emerald instead. If you want to use
compiz-manager and emerald in a script (eg. to start it right after the login)
use this line in your script:
# USE_EMERALD=yes compiz-manager