I'm suddenly experiencing this problem too on Ubuntu 13.10, with a
Norwegian keyboard. No problems during login, only after logging in.

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https://bugs.launchpad.net/bugs/985065

Title:
  Can't use fr/oss keyboard layout by default

Status in Release Notes for Ubuntu:
  Fix Released
Status in central project for keyboard configuration:
  Fix Released
Status in “xkeyboard-config” package in Ubuntu:
  Fix Released
Status in “xkeyboard-config” source package in Precise:
  Fix Released

Bug description:
  [Impact]
  The fr(oss) keyboard layout (and a couple others) fail to load, leaving the 
user with a US layout.

  [Development Fix]
  In the upstream bug tracker is a patch from Peter Hutterer which identifies a 
flaw in the ossmath map (which is included in keypad(oss), which is in turn 
pulled in by fr(oss)).  This patch has been included in Quantal.

  [Stable Fix]
  Same patch as in quantal is proposed here.

  [Test Case]
  1. Add the French (alternative) layout as first listed before US.
  2. Reboot
  3. After rebooting, the indicator menu shows French (alternative) selected.
  4. On a US keyboard, tap the 'm' key

  Broken Behavior: 'm' is printed, as per the US keymap
  Fixed Behavior: ',' is printed, as per the fr(oss) keymap

  [Regression Potential]
  The patch has not been committed to the upstream git tree; I usually like to 
see it taken upstream before we take it in ubuntu, but the patch itself seems 
to be good.  Still, I'm hoping we'll see upstream commit the patch before we 
roll this out to -updates.

  ossmath is included in a number of keymaps (although far from all), so
  the impact of a regression would be larger than just users of fr(oss).

  [Original Report]
  This is a break-out bug from bug 960096.  Also ref 
https://bugs.freedesktop.org/show_bug.cgi?id=47671

  When you have fr/oss "French (alternative)" layout as your first
  layout, you end up with "us" instead.

  If you enable libxklavier debugging output, you'll see the following
  in your logs:

  "Unexpected by libxklavier X ERROR: 0x8351fb8, 163f0005, 2 [], X11
  request: 145, minor code: 9"

                  xkl_debug(200,
                            "Unexpected by libxklavier X ERROR: %p, "
                            WINID_FORMAT ", %d [%s], "
                            "X11 request: %d, minor code: %d\n", dpy,
                            (unsigned long) evt->resourceid,
                            (int) evt->error_code, buf,
                            (int) evt->request_code, (int) evt->minor_code);

  That 2 in there is the X error code, which means _XkbErrMissingTypes
  for xkbfile extension. I assume 145 is the major op code that got
  assigned for the XKBFile extension. If so, 9 is the X_kbSetMap
  request. Which all fits with an error trying to set the new layout
  map.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: xorg 1:7.6+12ubuntu1
  ProcVersionSignature: Ubuntu 3.2.0-23.36-generic-pae 3.2.14
  Uname: Linux 3.2.0-23-generic-pae i686
  .tmp.unity.support.test.0:

  ApportVersion: 2.0.1-0ubuntu4
  Architecture: i386
  CheckboxSubmission: 9a284f3f6b4f7829abbe27ad9573a709
  CheckboxSystem: 3935143777c965daaa64b51f0134f712
  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]
  CompositorRunning: compiz
  Date: Wed Apr 18 12:31:05 2012
  DistUpgraded: 2011-11-05 19:49:52,977 DEBUG enabling apt cron job
  DistroCodename: precise
  DistroVariant: ubuntu
  DkmsStatus: virtualbox, 4.1.12, 3.2.0-23-generic-pae, i686: installed
  EcryptfsInUse: Yes
  ExtraDebuggingInterest: Yes, whatever it takes to get this fixed in Ubuntu
  GraphicsCard:
   Intel Corporation Core Processor Integrated Graphics Controller [8086:0046] 
(rev 18) (prog-if 00 [VGA controller])
     Subsystem: CLEVO/KAPOK Computer Device [1558:3100]
  InstallationMedia: Ubuntu 11.04 "Natty Narwhal" - Release i386 (20110422)
  Lsusb:
   Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
   Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
   Bus 001 Device 002: ID 8087:0020 Intel Corp. Integrated Rate Matching Hub
   Bus 002 Device 002: ID 8087:0020 Intel Corp. Integrated Rate Matching Hub
  MachineType: System76, Inc. Lemur UltraThin
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.2.0-23-generic-pae 
root=UUID=0e585e80-16f1-404c-80cc-7d9805fcc3b0 ro quiet splash vt.handoff=7
  SourcePackage: xorg
  UpgradeStatus: Upgraded to precise on 2011-11-05 (164 days ago)
  dmi.bios.date: 11/11/2010
  dmi.bios.vendor: Phoenix Technologies LTD
  dmi.bios.version: CALPELLACRB.86C.0000.X.0000000000
  dmi.board.asset.tag: Tag 12345
  dmi.board.name: Lemur UltraThin
  dmi.board.vendor: System76, Inc.
  dmi.board.version: lemu2
  dmi.chassis.asset.tag: No Asset Tag
  dmi.chassis.type: 10
  dmi.chassis.vendor: System76, Inc.
  dmi.chassis.version: lemu2
  dmi.modalias: 
dmi:bvnPhoenixTechnologiesLTD:bvrCALPELLACRB.86C.0000.X.0000000000:bd11/11/2010:svnSystem76,Inc.:pnLemurUltraThin:pvrlemu2:rvnSystem76,Inc.:rnLemurUltraThin:rvrlemu2:cvnSystem76,Inc.:ct10:cvrlemu2:
  dmi.product.name: Lemur UltraThin
  dmi.product.version: lemu2
  dmi.sys.vendor: System76, Inc.
  version.compiz: compiz 1:0.9.7.6-0ubuntu1
  version.libdrm2: libdrm2 2.4.32-1ubuntu1
  version.libgl1-mesa-dri: libgl1-mesa-dri 8.0.2-0ubuntu3
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 8.0.2-0ubuntu3
  version.xserver-xorg-core: xserver-xorg-core 2:1.11.4-0ubuntu10
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.7.0-0ubuntu1
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 
1:6.14.99~git20111219.aacbd629-0ubuntu2
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.17.0-1ubuntu4
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:0.0.16+git20111201+b5534a1-1build2

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