@saivinob, in my PC the values appears just like yours. Both are "defaoult" values:
> ginko@ginko:~$ gsettings get org.gnome.desktop.wm.keybindings close
> ['<Alt>F4']
> ginko@ginko:~$ gsettings get org.mate.Marco.window-keybindings close
> '<Alt>F4'
Is not silly; when I press the Alt+F4 combination nothing happens. But, Ctl+Q does close the windows. I also think Alt+F4 was assigned to some other action, but I really don't know how to find the conflict.
Lets wait, maybe somebody knows this issue, jeje.