As a workaround if you use .Xmodmap then I've found that renaming it and
loading it in startup applications instead works well.
mv .Xmodmap .Xmodmap_workaround
Open Startup Applications then click Add
In the command box enter xmodmap ~/.Xmodmap_workaround
Click Add then log out and in to see the effect.
When the problem is resolved don't forget to rename your Xmodmap back
and remove the entry in startup application.
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https://bugs.launchpad.net/bugs/649809
Title:
the session settings manager can try starting before the login screen
one exits
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