$HOME/.Xmodmap is applied twice in Xubuntu 12.04 LTS, I'm afraid. The
error messages I find in $HOME/.xsession-errors are the same I get when
running xmodmap twice on the command line (without any $HOME/.Xmodmap
present at login). By the same test, it is applied once in Ubuntu 14.04
LTS, both for 2D end 3D xsessions. My test:

tme@thinkpad-t43:~$ uname -a
Linux thinkpad-t43 3.2.0-27-generic #43-Ubuntu SMP Fri Jul 6 14:46:35 UTC 2012 
i686 i686 i386 GNU/Linux

tme@thinkpad-t43:~$ grep xmodmap .xsession-errors
[no matches]

tme@thinkpad-t43:~$ cat .Xmodmap
cat: .Xmodmap: No such file or directory

tme@thinkpad-t43:~$ cat .Xmodmap-backup 
!
!
! Make the right ctrl key behave as the windows key
!
remove control = Control_R
add Mod4 = Control_R
!
!
! Make the caps lock key behave as the shift key
!
remove lock = Caps_Lock
keysym Caps_Lock = Shift_L

tme@thinkpad-t43:~$ xmodmap .Xmodmap-backup 
[no errors]

tme@thinkpad-t43:~$ xmodmap .Xmodmap-backup 
xmodmap:  .Xmodmap-backup:11:  bad keysym in remove modifier list 'Caps_Lock', 
no corresponding keycodes
xmodmap:  .Xmodmap-backup:12:  bad keysym target keysym 'Caps_Lock', no 
corresponding keycodes
xmodmap:  2 errors encountered, aborting.

tme@thinkpad-t43:~$ mv .Xmodmap-backup .Xmodmap

tme@thinkpad-t43:~$ 
[logout and login again]

tme@thinkpad-t43:~$ grep xmodmap .xsession-errors
xmodmap:  /home/tme/.Xmodmap:11:  bad keysym in remove modifier list 
'Caps_Lock', no corresponding keycodes
xmodmap:  /home/tme/.Xmodmap:12:  bad keysym target keysym 'Caps_Lock', no 
corresponding keycodes
xmodmap:  2 errors encountered, aborting.

tme@thinkpad-t43:~$

-- 
You received this bug notification because you are a member of Desktop
Packages, which is subscribed to gdm in Ubuntu.
https://bugs.launchpad.net/bugs/700309

Title:
  $HOME/.Xmodmap is applied twice

Status in “gdm” package in Ubuntu:
  Expired

Bug description:
  Binary package hint: gdm

  It seems that $HOME/.Xmodmap is applied twice in Ubuntu 10.10. This
  might cause problems for some users - in my case, for example, I use
  Xmodmap to swap the Escape and CapsLock key - so when applied twice,
  nothing is essentially swapped. FYI, here's my .Xmodmap:

      ! Swap caps lock and escape
      remove Lock = Caps_Lock
      keysym Escape = Caps_Lock
      keysym Caps_Lock = Escape
      add Lock = Caps_Lock

  I verified this by commenting out the line in /etc/gdm/Xsession which
  applies my ".Xmodmap". After that, everything works as expected. It
  seems that some other component applies .Xmodmap, too - I guess it's
  some part of Gnome, as sometimes when logging in I get asked which
  .Xmodmap I want to load.

To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/gdm/+bug/700309/+subscriptions

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