There have been significant changes in Xorg and the handling of input devices.
It is possible that through these changes things changed that affect your
layout.
What I suggest,
'xmodmap' keyboard layouts are uncommon and show a degree of expertise in
Xorg.
In this respect, I suggest to take this issue to https://bugs.freedesktop.org/
and file a report them. You may also perform searches for existing reports on
xmodmap there.
I am closing this report as it did not have an update since 2008.
** Changed in: xkeyboard-config (Ubuntu)
Status: Confirmed => Invalid
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xmodmap confuses keyboard layout in gnome
https://bugs.launchpad.net/bugs/268967
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