Ubuntu 16.04.1 settings changing but getting ignored

I've recently update Ubuntu 16.04 using the dist-upgrade commands. Some settings suddenly stopped working, such as Workspaces, Launcher placement (always display on all monitors) and sticky edge is always on.

I've formatted, reinstalled Ubuntu 16.04, everything works until I run dist-upgrade (16.04.1), then after reboot the problems return. I decided to reinstall 16.04 and update package by package to pinpoint which one was causing the issue. The issue appeared after upgrading the unity package.

If I run these commands:

dconf read /org/compiz/profiles/unity/plugins/unityshell/num-launchers

Will return the right value, either 1 (if I set launcher on one screen) or 0 (if I set the launcher on all screens).

dconf read /org/compiz/profiles/unity/plugins/core/hsize
dconf read /org/compiz/profiles/unity/plugins/core/vsize

Both return 2 (if I tick Enable Workspaces) or 1 (if I untick Enable Workspaces)

So the settings actually get changed, but they are getting ignored for some reason?