I'm having a problem with my default Gnome 3.6.0 setup on 12.10. I used to create themes in Gnome 2 and Gnome 3.0, but I'm at loss to explain why my theme is black in the background. This problem is limited to Adwaita, and there are not any issues with Ambiance or Radience. I guess it isn't a really big deal because I'm going to upgrade soon, but until then Gnome is going to be looking pretty ugly; almost unusable.
2 Answers
By your screenshots, I am able to see that you are also using the Unity scroll-bar overlay. This unfortunately has a known bug with this theme and package.
Use sudo apt-get remove overlay-scrollbar*
to remove the overlay-scrollbars from the system and it should resolve this issue.
Maybe a bit of a long shot, but I used Gnome Color Chooser (http://gnomecc.sourceforge.net/) to make the black hint pop-ups in eclipse yellow (in 12.04) - maybe you can use it to fix your background.