There are several programs that might draw a background, and sometimes more than one get drawn one on top of the other.
If you intstall dconf-tools and navigate to "org > gnome > desktop > background" (as your usual user), you can choose to have gnome draw a background and set the path to whatever image you want. On my system, (Ubuntu 13.04, GNOME 3.6, classic session with compiz), that is the background that I see in my lock screen (the default in Ubuntu 13.04, gnome-screensaver).
Nautilus can draw it's own background too up to GNOME 3.6, and, if I remember correctly, it needs to in order to offer file/folder context menus, along whith it's own dconf-editor/gsettings flag. BUT that is gone in GNOME 3.8 (see this launchpad bug for more info).
Also, compiz can also draw it's own background(s), you can get there through ccsm (compiz config settings manager, google it in the rare case that you don't already know it). I use this solution because it lets me have a different background in each viewport/desktop.
In regard to ubuntu tweak, it is a known issue that it has trouble with GNOME 3.8, and it seems that it targets support (as is understandable) for the current ubuntu release, of which GNOME 3.6 is a too sensible component to fiddle with for what I would call a "stable" graphical interface (I had some other theme and application issues when I tried it a while ago in this same system).
I would tend to advise you to stay on GNOME 3.6 while you are un Ubuntu 13.04, but be careful whith the downgrade if you choose to do so, I remember it to be tricky.