Just did some testing (with two gEdit windows) this morning, Ubuntu
14.04 updated to the latest packages as of today (2014-04-01). I apt-get
installed ubuntu-gnome-desktop and kubuntu-desktop on a regular Ubuntu
14.04 install.

GNOME desktop (gnome-shell): Both gEdit windows can be scrolled with the 
pointer hovering over the window, regardless of focus.
GNOME desktop classic (I guess still gnome shell?): Same as GNOME desktop, 
scrolling works while hovering, regardless of focus.
KDE plasma desktop: gEdit window needs to be focused to be scrolled
Ubuntu Unity desktop: gEdit window needs to be focused to be scrolled

And on Ubuntu 14.04 (around beta 1 packages) on a netbook with a
touchpad and mouse connected: Nautilus windows can be scrolled with the
touchpad while hovering, regardless of focus, but NOT with the mouse.

So, what makes the gnome-shell desktop different to Unity and KDE? The X
server, GTK etc are all the same.

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https://bugs.launchpad.net/bugs/1240957

Title:
  Scrolling behaviour and window focus has changed and is inconsistent

Status in GTK+ GUI Toolkit:
  Fix Released
Status in X.Org X server:
  Confirmed
Status in “gtk+3.0” package in Ubuntu:
  Fix Released
Status in “xorg-server” package in Ubuntu:
  Triaged

Bug description:
  I wasn't sure which package to file this bug against, but seeing as
  it's a general desktop usability/consistency bug, the top level
  desktop environment seemed like a good target.

  On Ubuntu 13.10, AMD64, everything default (Unity 7 on X.org etc),
  except for installing nvidia-319-updates, all current packages as of
  now (2013-10-17; unity 7.1.2+13.10.20131014.1-0ubuntu1), I now have
  this behaviour which is different from Ubuntu versions up to 13.04,
  and, is also inconsistent within itself. Here's what I've found:

  The scrolling behaviour has changed, and seems to be different per
  application in Ubuntu 13.10.

  The old behaviour (up to 13.04): mouse pointer above window would allow 
scrolling, regardless of focus
  Apps that use the old behaviour: libreoffice, firefox, gnome-terminal

  The new behaviour (13.10): window must be focused, and pointer hovered above 
to allow scrolling
  Apps that use the new behaviour: nautilus, gedit, ubuntu-bug, software-updater

  
  STEPS TO REPRODUCE

  1. Open gEdit, press enter until the window is scrollable.
  2. Open Firefox, go to a webpage that's scrollable.
  3. Place gEdit above Firefox but off to the right side so gEdit's scrollbar 
is still visible, have gEdit focused.
  4. Position mouse pointer above gEdit, observe scrollwheel causes gEdit 
window to scroll.
  5. Move mouse pointer above Firefox but do not focus Firefox, observe 
scrollwheel causes Firefox window to scroll.
  6. Focus Firefox, leave pointer above Firefox, observe scrollwheel causes 
Firefox window to scroll
  7. Move mouse pointer above gEdit but do not focus gEdit, observe scrollwheel 
FAILS to cause gEdit window to scroll.

  
  This behaviour is the same with any combination of the above apps 
(libreoffice, firefox, gnome-terminal all scrollable as long as pointer is 
above them; nautilus, gedit, software-updater, ubunut-bug will not scroll 
unless focused *and* have pointer above them)

  What *SHOULD* happen, is that any window will scroll as long as the
  pointer is above it. That's how it's always been in Ubuntu.

  ProblemType: Bug
  DistroRelease: Ubuntu 13.10
  Package: unity 7.1.2+13.10.20131014.1-0ubuntu1
  ProcVersionSignature: Ubuntu 3.11.0-12.19-generic 3.11.3
  Uname: Linux 3.11.0-12-generic x86_64
  NonfreeKernelModules: nvidia
  ApportVersion: 2.12.5-0ubuntu2
  Architecture: amd64
  CompizPlugins: No value set for 
`/apps/compiz-1/general/screen0/options/active_plugins'
  Date: Thu Oct 17 22:12:18 2013
  InstallationDate: Installed on 2013-09-30 (17 days ago)
  InstallationMedia: Ubuntu 13.10 "Saucy Salamander" - Beta amd64 (20130925.1)
  MarkForUpload: True
  SourcePackage: unity
  UpgradeStatus: No upgrade log present (probably fresh install)

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