Since the above fix was only for Hardy, I'll post the workaround I found
for Gutsy. I needed this for the extra keys on my Logitech G11 keyboard.

Background:
As mentioned before, Xfce's xinitrc calls xfce-session, which calls 
xfce-mcs-manager. And this is the program that is using xkbcomp to override 
.Xmodmap. The problem is that xfce-mcs-manager is called as pretty much the 
last step in xfce-session (even after Xfce's autostarted programs list, and the 
ClientN_Command lines in xfce4-session.rc), and xfce-session does not actually 
complete until you log out of Xfce (obviously.) So there's no place to ask Xfce 
to load a custom .Xmodmap without having it overridden, short of modifying the 
sources to xfce-session and/or xfce-mcs-manager.

Workaround:
Since xfce-mcs-manager is causing the problem, we can replace it with a small 
shell script that will execute it, and then load the .Xmodmap file upon 
completion. The following commands will work:

cd /usr/bin
sudo mv xfce-mcs-manager xfce-mcs-manager-bin
sudo mousepad xfce-mcs-manager
sudo chmod 0755 xfce-mcs-manager

After the third line, you'll obviously get a blank mousepad window. Add
the following to it and then save the file:

#!/bin/sh
xfce-mcs-manager-bin
test -r $HOME/.Xmodmap && xmodmap $HOME/.Xmodmap

... and follow with the chmod command to mark the new script as
executable. Log out and back in, and your custom .Xmodmap should still
be active. Verify with xev, if you like.

I understand this may not be the desirable way to fix this problem. But
it works, and doesn't break anything (as chmod 0644 xkbcomp does.)

Hope this helps.

-- 
[xubuntu only]xfce4-session seems to reset xmodmap
https://bugs.launchpad.net/bugs/97175
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