I upgraded to Ubuntu 11.10 today, which seems to have done a nice enough job of integrating GNOME 3.2, but I was instantly driven mad by all of my GNOME Terminals showing their menubars, in what appeared to be direct contravention of what the setting appeared to be (or even what GTK+ thought the visibility status of the widget was!). This was GNOME bug #658760.
After a stack of debugging and one lucky break, I discovered the culprit was infact Ubuntu’s appmenu module.
[The lucky break was that while setting up a bisect, I realised I could replicate the bug only in the GTK+ 3 build of the terminal, which was printing out warnings about appmenu, something I'd already uninstalled for GTK+ 2.]
Anyway, you can fix the problem by removing appmenu-gtk3 (personally I’d remove appmenu-*) or unsetting the environment variable UBUNTU_MENUPROXY which is set in /etc/Xsession.d/80appmenu or something. The Ubuntu bug is #879190.
Random side note: can someone update my hackergotchi please?