Bug 1367764, seems to have narrowed down the cause and come close to
finding a solution.

** Description changed:

  When Ayatana overlay-scrollbar is enabled, GtkScrolledWindow widgets may
  be rendered without a background.
  
  Without composting these areas are black (openbox, gnome-shell) and with
  composting they are transparent (compiz, compton). Other visual glitches
  include content within the widget not clearing on redraw (everything
  becomes a cluttered mess) and with composting any content appearing
  under the transparent area on initial window mapping is retained (as if
  that were the widget background).
  
  For example, pavucontrol: https://ibb.co/eiRcBF
  
- Original description:
- Some GTK widgets have a black background. So far I have noticed this 
happening in g-c-c, gedit tab bar and dconf-editor details pane. This only 
happens when the applications are launched from gnome-shell, they work 
correctly when launched from a terminal.
+ Description from duplicate bug 1367764:
+ The overlay scrollbar module forces the window that should be scrolled to be 
native. Gtk is moving away from native windows and seems to have some 
hard-to-find regressions when using them.
  
- I can reproduce on both my machines that were upgraded from Q, but not a
- fresh install.
+ This causes a bunch of themeing issues (black/transparent backgrounds)
+ which can be worked around in the theme by setting backgrounds for these
+ widgets explicitely. That's a performance issue (since we're filling
+ backgrounds unnecessarily) and annoying, as these have to be only some
+ of the time for some widgets (e.g., GtkEventBox).
  
- ProblemType: Bug
- DistroRelease: Ubuntu 13.04
- Package: libgtk-3-0 3.7.12-1ubuntu1~build1 [origin: LP-PPA-gnome3-team-gnome3]
- ProcVersionSignature: Ubuntu 3.8.0-16.26-generic 3.8.5
- Uname: Linux 3.8.0-16-generic x86_64
- NonfreeKernelModules: nvidia
- ApportVersion: 2.9.2-0ubuntu5
- Architecture: amd64
- Date: Wed Apr 10 10:09:44 2013
- InstallationDate: Installed on 2012-09-23 (198 days ago)
- InstallationMedia: Ubuntu GNOME Remix 12.10 "Quantal Quetzal" - Alpha 
amd64(20120922)
- MarkForUpload: True
- SourcePackage: gtk+3.0
- UpgradeStatus: No upgrade log present (probably fresh install)
+ Porting overlay-scrollbars to not use native windows might be worthwhile
+ if we decide to keep them.

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https://bugs.launchpad.net/bugs/1167079

Title:
  GtkScrolledWindow widgets (GTK3) have black or transparent
  backgrounds with Ayatana overlay-scrollbar

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