Just out of curiosity, which DE or WM are you using?
Most of the time Trinity, sometimes KDE4. The biggest culprit of the popup menu is kate/kwrite. Bumping the right Win key (Super_R?) is the same as a "right-click" in kate/kwrite. which invokes a context popup menu. I get the same behavior in KDE4 kate.
That said I tried adding /etc/X11/xinit/Xmodmap:
# disable the left win key
keycode 133 =
# disable the right win key
keycode 135 =
I tried ~/.Xmodmap and adding the xmodmap -e command in a desktop file in autostart. None of that works.
I still get the popup menu in kate, both Trinity and KDE4.
Yet I always could execute the xmodmap -e command in a terminal window and succeed.
Then I discovered that directly running 'xmodmap /etc/X11/xinit/Xmodmap' in a terminal window resulted in complaints. Oh. So I remove the comments in /etc/X11/xinit/Xmodmap. After removing the comments the file worked as intended when I started X.
Oh, wait! Comments in this file are marked by an exclamation mark, not a hash mark.
The damned Win keys now are impotent.
The Xmodmap file works in Trinity but not KDE4. Almost exact same xinit scripts. Both scripts run the command 'xmodmap /etc/X11/xinit/Xmodmap'.
I can run 'xmodmap /etc/X11/xinit/Xmodmap' manually in a terminal window and the commands work in KDE4.
I can copy /etc/X11/xinit/Xmodmap to ~/.Xmodmap then the commands work in KDE4.
But from /etc/X11/xinit/Xmodmap KDE4 balks. Trinity plays ball.
I am clueless.
I picked the wrong week to stop sniffing glue. Next I'll discover I have a drinking problem. And that everybody is counting on me. Where is my auto-pilot?
P.S. Yes, I edited my xinit scripts to use /etc/X11/xinit/Xmodmap and not /etc/X11/xinit/.Xmodmap.