I know a little more now:
I straced xfce4-session from the xinitrc.  In the output, there was a 
suspicious call to xkbcomp.  So I removed the executable bit from 
/usr/bin/xkbcomp, and voilĂ , my .Xmodmap works.  I'll try reverting to a 
previous version of xkb-data and xkb-utils next.

-- 
xfce4-session seems to reset xmodmap
https://launchpad.net/bugs/97175

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