Here's a backtrace from when the options get reset, but I can't quite make sense of it. It looks like compiz gets notified that the gsettings key 'org.compiz.core close-window-key' (which I can't find in dconf-editor!) got changed. As a response to that it sets 'org.gnome.desktop.wm.keybindings close' to the new value (which happens to be the default value), thereby overwriting the user-set value. Which I think would be a terrible idea even if the user had intentionally changed close-window-key.
Here's a backtrace from when the options get reset, but I can't quite make sense of it. It looks like compiz gets notified that the gsettings key 'org.compiz.core close-window-key' (which I can't find in dconf-editor!) got changed. As a response to that it sets 'org.gnome. desktop. wm.keybindings close' to the new value (which happens to be the default value), thereby overwriting the user-set value. Which I think would be a terrible idea even if the user had intentionally changed close-window-key.