Global menu broken after an update

Also, this might be helpful: I am using pantheon-files daily builds, instead of Nautilus, but I doubt that should be causing any problem (I tried removing pantheon-files and all of its configuration files, but that doesn't help). I've also tried removing appmenu-gtk3, appmenu-gtk, appmenu-qt and indicator-appmenu, then removing all config files, and reinstalling, but that didn't help. All the settings seem to be set properly in dconf-editor (i.e., menu type is set to "global" and hud is in use).

Where are you getting the daily build from?

Well, for pantheon-files I was getting daily builds from ppa:elementary-os/daily, but I have uninstalled pantheon-files and removed all its config files. As far as Ubuntu, I only get regular updates (security updates and regular releases), no daily builds.

Also, another interesting thing that happened after those updates is this: now when I right click on the desktop and select "Change Desktop Background", instead of the "Appearance" dialog, I get "System Settings" window (from which I can of course get to Appearance by clicking "Appearance").

When I run "apt-get upgrade", I get:

The following packages have been kept back:
  gnome-control-center gnome-control-center-data

I am also using ppa:gnome3-team/gnome3

to have gnome 3.6.

Well , you have added PPAs that upgrade essential system packages (like the Gnome PPA) so is not weird that some time the environment can crash.
As for the kept back message , try this command

~$ sudo apt-get dist-upgrade

Thanks

Thanks guys. I just purged ppa:gnome3-team and reverted back to the previous version. That fixed all the problems.

I have the same issue. I purged the Gnome-3-team PPA , re-updated, dist-upgraded but still have the same issue.
What do you mean by reverted to the previous version???

OK. Problem solved by using the latest ppa-purge package.