I am having the same issue, with gedit and evince not scrolling with
mouse wheel, except it is when the keyboard focus in on another window
(e.g. terminal) but mouse focus is on the first window (I am not sure
what precisely is meant by mouse being hidden, so I cannot confirm this
aspect). I do not have this issue with gnome-terminal or chromium.

I have just upgraded from 12.10 to 13.10 (via 13.04) and this is when
the issue started occurring.

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https://bugs.launchpad.net/bugs/1246000

Title:
  gtk text widget ignores the mouse wheel

Status in “unclutter” package in Ubuntu:
  New

Bug description:
  In evince, gitg, gedit when the mouse is hidden using the wheel make the 
mouse flash
  but do not scroll down or up.

  ii  unclutter                                             8-19
  ii  libgtk-3-0:i386                                       3.8.6-0ubuntu2

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