After further testing I can safely say that it's not window manager related. Mutter(gnome-shell), Compiz(unity), metacity(unity) all have the same problem. I can activate the emulation for the session only and after suspend or shutdown the setting is gone. Well it's still marked in the gpointing-device-settings window it just doesn't work anymore till you toggle the switch.
After further testing I can safely say that it's not window manager related. Mutter( gnome-shell) , Compiz(unity), metacity(unity) all have the same problem. I can activate the emulation for the session only and after suspend or shutdown the setting is gone. Well it's still marked in the gpointing- device- settings window it just doesn't work anymore till you toggle the switch.