I had this problem in Ubuntu 13.04, then later in 13.10 (upgraded from
13.04) on multiple occasions - usually this happens at least twice a
week.

Possible ways to handle it (for people who come across this via search) till it 
gets fixed:
1) Press Alt-F2, then type 'unity'. Unity will reset (all the windows will go 
to the first workspace), and the launcher will auto-hide once more. 
(Recommended option)

2) Set Launcher autohide in System Settings > Appearance> Behavior to false, 
launcher will no longer autohide, but at least the applications will no longer 
render to fill the space under the launcher.
Once you are done with your work, either do the same as (1), or logout and log 
back in, or restart, the turn autohide back on

3) If you are not doing any serious work, just logout and log back in or
restart.

In regards to cause of the problem, I don't think touchscreens are an
issue, none of my devices running full Ubuntu had a touchscreen.

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https://bugs.launchpad.net/bugs/1158107

Title:
  launcher does not hide when auto-hide is enabled

Status in “unity” package in Ubuntu:
  Confirmed

Bug description:
  After upgrading to raring, the launcher never auto-hides, even with
  the "Auto-hide the Launcher" setting is enabled. When the setting is
  toggled, maximized windows resize to fit the full as if the launcher
  were hidden, but it never disappears.

  ProblemType: Bug
  DistroRelease: Ubuntu 13.04
  Package: unity 6.12.0daily13.03.13.1-0ubuntu1
  ProcVersionSignature: Ubuntu 3.8.0-13.22-generic 3.8.3
  Uname: Linux 3.8.0-13-generic x86_64
  NonfreeKernelModules: wl
  ApportVersion: 2.9.2-0ubuntu1
  Architecture: amd64
  CompizPlugins: 
[core,composite,opengl,compiztoolbox,decor,vpswitch,snap,mousepoll,resize,place,move,wall,grid,regex,imgpng,session,gnomecompat,animation,fade,unitymtgrabhandles,workarounds,scale,expo,ezoom,unityshell]
  Date: Wed Mar 20 22:49:59 2013
  EcryptfsInUse: Yes
  InstallationDate: Installed on 2012-09-17 (184 days ago)
  InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Release amd64 
(20120425)
  MarkForUpload: True
  ProcEnviron:
   TERM=xterm
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: unity
  UpgradeStatus: Upgraded to raring on 2013-03-19 (1 days ago)

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