Hi,
It looks like gnome xsettings daemon was not starting. I also asked at the Gnome forum when I was getting stuck, where it was mentioned about the xsettings manager. (Is the default desktop theme backed up outside /usr/share/themes? - #4 by matthiasc - Desktop - GNOME Discourse)
Adding /usr/libexec/gsd-xsettings to the autostart programmes fixed the issue, although I am not sure how it came to be broken.
Thanks,
L