@Ikuya: I found that gnome-settings-daemon 3.18, which is in the Xenial archive, also overrides those two variables. So my guess is that you had 3.20 on your Xenial installation. (If not, this is still a mystery.)
Anyway, I prepared merge proposals for gnome-session (Yakkety and Xenial), and attached a Xenial patch for gnome-settings-daemon.
@Ikuya: I found that gnome-settings- daemon 3.18, which is in the Xenial archive, also overrides those two variables. So my guess is that you had 3.20 on your Xenial installation. (If not, this is still a mystery.)
Anyway, I prepared merge proposals for gnome-session (Yakkety and Xenial), and attached a Xenial patch for gnome-settings- daemon.